Re: [gmx-users] Constant-Force Pulling of Ubiquitin
You want to switch to sd instead of md. On Oct 29, 2013, at 17:43, Vivian ww...@bu.edu wrote: Hi GMX Users, I am using Gromacs (Version 4.5.5) to do constant-force pulling of ubiquitin and it's a implicit model. My mdp file for pulling is shown as following. integrator = md dt = 0.001; ps ! nsteps = 50 ; total 500 ps. nstxout = 100 nstvout = 100 nstfout = 100 nstlist = 10 nstlog = 100 nstcalcenergy=100 rlist = 5 rvdw = 5 rcoulomb = 5 coulombtype = cut-off vdwtype = cut-off table-extension = 5 bd_fric = 0 ld_seed = -1 pbc = no ns_type = simple constraints = all-bonds lincs_order = 4 lincs_iter = 1 lincs-warnangle = 30 Tcoupl = v-rescale tau_t = 1.0 tc-grps = Protein ref_t = 300 Pcoupl = no gen_vel = yes gen_temp= 300 gen_seed= 173529 comm_mode = Angular nstcomm =100 ; IMPLICIT SOLVENT ALGORITHM implicit_solvent = gbsa ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 5 ; Dielectric coefficient of the implicit solvent gb_epsilon_solvent = 80 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; Scaling factors used in the OBC GB model. Default values are OBC(II) gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 gb_dielectric_offset = 0.009 sa_algorithm = Ace-approximation ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA ; The value -1 will set default value for Still/HCT/OBC GB-models. sa_surface_tension = 2.05016 ; Pull code pull= constant_force ;Center of mass pulling using a linear potential and therefore a constant force. pull_geometry = direction pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group1 = Chain_B pull_group0 = Chain_A pull_k1 = -500 ; kJ mol^-1 nm^-2 pull_vec1 = 0.0 0.0 1.0 However, after pulling simulation, it turns out the potential of this system becomes lower rather than higher (from -1 to -2). It's very wired since potential should become larger after pulling. Here is the notification after g_energy: Energy Average Err.Est. RMSD Tot-Drift --- Potential -20734.52301268.47 -1385.71 (kJ/mol) You may want to use the -driftcorr flag in order to correct for spurious drift in the graphs. Note that this is not a substitute for proper equilibration and sampling! You should select the temperature in order to obtain fluctuation properties. I wonder whether there is any problem with my mdp file. Thank you so much!! Best, Vivian -- View this message in context: http://gromacs.5086.x6.nabble.com/Constant-Force-Pulling-of-Ubiquitin-tp5012065.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Is the website of Martini Force Field down for maintenance?
Try cgmartini.nl On Oct 16, 2013, at 10:29 PM, 朱文鹏 jasonzhu...@gmail.com wrote: Dear GMX users, I am going to do some coarse-grained simulations in which the lipid bilayeris covered by polysarccharide. I remember the website of Martini Force Field (http://md .chem.rug.nl/cgmartini/) provides a database for sugar including .itp and . gro files of long chains of different polysarccharide. But I can not open the website now. Is it down for maintenance or changed to another address? Do you have these .itp and .gro files of polysarccharidefor Martini Force Field? Thank you very much for your help. Best, Jason -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] default -rdd with distance restraints seems too large
Yes it is a pity! But particle decomposition helps :)) well helped! It's a shame that long distance restraints limit the parallalization so much, but it is understandable. Thanks for helping me with this. Chris. -- original message -- Initializing Domain Decomposition on 8 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 2.636 nm, Dis. Rest., atoms 1701 4425 multi-body bonded interactions: 0.479 nm, CMAP Dih., atoms 1062 1081 Minimum cell size due to bonded interactions: 2.899 nm Maximum distance for 7 constraints, at 120 deg. angles, all-trans: 1.172 nm Estimated maximum distance required for P-LINCS: 1.172 nm Using 0 separate PME nodes, as there are too few total nodes for efficient splitting Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 8 cells with a minimum initial size of 3.624 nm The maximum allowed number of cells is: X 1 Y 1 Z 2 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] default -rdd with distance restraints seems too large
Hi Chris, I mentioned that PS would have helped! I am sorry about the confusion. I should have been more clear. I guess you have not followed the particle decomposition threads lately :)) The PD option has been associated some serious issues lately … notably I noticed it does not work well in combination of REMD. Some info is not communicated correctly and thus a few variables are wrong. I forgot which ones … Most recently Floris (a PhD student with us in Groningen) has noticed that turning PD on would lead to severe buckling of a membrane to the point that the system would crash. The is happening quite fast. If you can use an older version of GMX (4.0.7) this would be fine but starting 4.5.5 things are ugly :)) I hope this helps. On Oct 17, 2013, at 5:57 PM, Christopher Neale chris.ne...@mail.utoronto.ca wrote: Thanks for the hint XAvier. Unfortunately, I get crashes with particle decomposition (see below). If I use either DD or PD, I can run on up to 2 threads without adjusting -rdd or -dds. I can only use 2 thread with DD if I set -rdd 2.8. If I try to use more than 2 threads with PD, I get lincs problems and immediate crashes. If I export GMX_MAXCONSTRWARN=-1 with the same setup , then I get a segfault immediately. Note, however, that if I use constraints=none and set my timestep to 0.5 fs, I can indeed use PD with 8 threads (without exporting GMX_MAXCONSTRWARN). Also note that I am using the SD integrator, but I just tested and PD also gives me an error with the md integrator. (( I don't think that the crashes have anything to do with improper setup. These runs are fine in serial or in parallel as described above and only ever explode/crash with PD and 2 threads, for which they do so immediately )). Here is the error that I get when I Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 218.843810, max 8135.581543 (between atoms 15623 and 15624) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 13908 13916 90.80.2130 0.8066 0.1538 13916 13917 90.30.2402 0.7979 0. 13916 13918 90.20.2403 0.8452 0. 13916 13919 89.31.3408 0.9956 0.1430 ... ... 22587 22589 31.70.4648 0.1144 0. 22587 22590 90.20.4168 0.1273 0. Wrote pdb files with previous and current coordinates starting mdrun 'Gallium Rubidium Oxygen Manganese Argon Carbon Silicon in water' 500 steps, 1.0 ps. WARNING: Listed nonbonded interaction between particles 13908 and 13920 at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. step 0: Water molecule starting at atom 39302 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. step 0: Water molecule starting at atom 53072 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 2569455308.447471, max 215672291328.00 (between atoms 14054 and 14055) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 13442 13444 90.00. 0.1147 0. 13503 13506 40.80.1538 0.2002 0.1538 13506 13507 45.20. 0.1541 0. ... ... 19020 19023 89.80.1534 66420.9531 0.1530 ;;dispcorr = EnerPres ;; not using for CHARMM simulations ### mdp options: constraints = all-bonds lincs-iter = 1 lincs-order = 6 constraint_algorithm = lincs integrator = sd dt = 0.002 tinit = 0 nsteps = 500 nstcomm = 1 nstxout = 500 nstvout = 500 nstfout = 500 nstxtcout = 500 nstenergy = 500 nstlist = 10 nstlog=0 ; reduce log file size ns_type = grid vdwtype = switch rlist = 1.2 rlistlong = 1.3 rvdw = 1.2 rvdw-switch = 0.8 rcoulomb = 1.2 coulombtype = PME ewald-rtol = 1e-5 optimize_fft = yes fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 tc_grps = System tau_t = 1.0 ld_seed = -1 ref_t = 310 gen_temp = 310 gen_vel = yes unconstrained_start = no gen_seed = -1 Pcoupl = berendsen pcoupltype =
Re: [gmx-users] recalculating .trr from .xtc
Interactions will be off, especially the bonded terms. On Oct 15, 2013, at 7:21, Mark Abraham mark.j.abra...@gmail.com wrote: Also, the precision was selected when the xtc file was written, ie in the mdp file. Mark On Oct 15, 2013 3:24 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/14/13 7:56 PM, Leandro Bortot wrote: Dear GROMACS users, Does anyone know how significant is the difference between the original .trr file from a simulation and a recalculated .trr from a whole system .xtc (mdrun -rerun traj.xtc -o traj.trr)? I mean... do you know how big would be the error induced by this recalculation procedure? I'm not interested in calculating autocorrelation functions. Most of my analysis are related to the atom positions over time and free energy calculations. Position-related quantities should be impacted very little. Given that you can't acquire precision though, I see no point in even generating a .trr file - the .xtc has the same information while occupying less disk space. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] energy drift - comparison of double and single precision
Could you try to reduce the nstcalcenergy flag from 100 to 10 and then one? Similar flags apply to temperature and pressure and I believe might seriously affect energy conservation. XAvier. On Oct 12, 2013, at 0:50, Mark Abraham mark.j.abra...@gmail.com wrote: Didn't see any problem in the .mdp. -4500 kJ/mol in 10ns over (guessing) 30K atoms is 0.015 kJ/mol/ns/atom. k_B T is at least 100 times larger than that. I bet the rest of the lysozyme model physics is not accurate to less than 1% ;-) There are some comparative numbers at http://dx.doi.org/10.1016/j.cpc.2013.06.003 - the two systems are rather different but they share the use of SETTLE. Note that using md-vv guarantees the 2007 paper is inapplicable, because GROMACS did not have a velocity Verlet integrator back then. Sharing the .log files might be informative. Mark On Fri, Oct 11, 2013 at 11:38 PM, Guillaume Chevrot guillaume.chev...@gmail.com wrote: Hi, sorry for my last post! I re-write my e-mail (with some additional information) and I provide the links to my files ;-) I compared the total energy of 2 simulations: lysozyme in water / NVE ensemble / single precision / Gromacs 4.6.3 lysozyme in water / NVE ensemble / double precision / Gromacs 4.6.3 ... and what I found was quite ... disturbing (see the plots of the total energy: http://dx.doi.org/10.6084/m9.figshare.820153). I observe a constant drift in energy in the case of the single precision simulation. Did I do something wrong*? Any remarks are welcomed! Here is the link to the ‘mdout.mdp’ file (http://dx.doi.org/10.6084/m9.figshare.820154) so you can check what mdp options I used. My second question is: if I did not do something wrong, what are the consequences on the simulation? Can I trust the results of single precision simulations? Regards, Guillaume *PS: I am not the only one encountering this behavior. In the literature, this problem has already been mentioned: http://jcp.aip.org/resource/1/jcpsa6/v126/i4/p046101_s1 2013/10/11 Mark Abraham mark.j.abra...@gmail.com On Oct 11, 2013 7:59 PM, Guillaume Chevrot guillaume.chev...@gmail.com wrote: Hi all, I recently compared the total energy of 2 simulations: lysozyme in water / NVE ensemble / single precision lysozyme in water / NVE ensemble / double precision ... and what I found was quite ... disturbing (see the attached figure - plots of the total energy). I observe a constant drift in energy in the case of the single precision simulation. Did I do something wrong*? Any remarks are welcomed! I join the ‘mdout.mdp’ file so you can check what mdp options I used. Maybe. Unfortunately we cannot configure the mailing list to allow people to send attachments to thousands of people, so you will need to do something like provide links to files on a sharing service. My second question is: if I did not do something wrong, what are the consequences on the simulation? Can I trust the results of single precision simulations? Yes, as you have no doubt read in the papers published by the GROMACS team. Regards, Guillaume *PS: I am not the only one encountering this behavior. In the literature, this problem has already been mentioned: http://jcp.aip.org/resource/1/jcpsa6/v126/i4/p046101_s1 ... which is six years old, examining the properties of code seven years old. Life has moved on! :-) Even if you have found a problem, it is a big assumption that this is (still) the cause. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list.
Re: [gmx-users] Performance of Gromacs-4.6.1 on BlueGene/Q
BG CPUs are generally much slower (clock whose) but scale better. You should try to run on 64 CPUs on the Blue gene too for faire comparison. The number of CPUs per nodes is also an important factor: the more CPUs per nodes the more communications needs to be done. I observed a significant slow down while going from 16 to 32 CPUs nodes (recent intel) but using the same number of CPUs. On Jun 4, 2013, at 4:02 PM, Jianguo Li ljg...@yahoo.com.sg wrote: Dear All, Has anyone has Gromacs benchmark on Bluegene/Q? I recently installed gromacs-461 on BG/Q using the following command: cmake .. -DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C \ -DGMX_BUILD_OWN_FFTW=ON \ -DBUILD_SHARED_LIBS=OFF \ -DGMX_XML=OFF \ -DCMAKE_INSTALL_PREFIX=/scratch/home/biilijg/package/gromacs-461 make make install After that, I did a benchmark simulation using a box of pure water containing 140k atoms. The command I used for the above test is: srun --ntasks-per-node=32 --overcommit /scratch/home/biilijg/package/gromacs-461/bin/mdrun -s box_md1.tpr -c box_md1.gro -x box_md1.xtc -g md1.log job_md1 And I got the following performance: Num. cores hour/ns 128 9.860 256 4.984 512 2.706 10241.544 20480.978 40920.677 The scaling seems ok, but the performance is far from what I expected. In terms CPU-to-CPU performance, the Bluegene is 8 times slower than other clusters. For comparison, I also did the same simulation using 64 processors in a SGI cluster, and I got 2.8 hour/ns, which is roughly equivalent to using 512 cores in BlueGene/Q. I am wondering if the above benchmark results are reasonable or not? Or Am I doing something wrong in compiling? Any comments/suggestions are appreciated, thank you very much! Have a nice day! Jianguo -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: REMD analysis
Well use a regular plotting software and look at it or do some more elaborated operation in or out the software to estimate the overlap :)) On May 17, 2013, at 1:14 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, I ran the REMD simulation with temp. distribution discussed in my last thread. Each replica was run for 50 ns Replica exchange statistics Repl 24999 attempts, 12500 odd, 12499 even Repl average probabilities: Repl 0123456789 10 11 12 Repl .22 .19 .18 .16 .19 .21 .23 .25 .26 .29 .28 .28 Repl number of exchanges: Repl 0123456789 10 11 12 Repl 2661 2369 2296 2008 2360 2668 2866 3119 3234 3549 3469 3475 Repl average number of exchanges: Repl 0123456789 10 11 12 Repl .21 .19 .18 .16 .19 .21 .23 .25 .26 .28 .28 .28 Now, how to find the potential energy overlap for each replica??.. I have obtained the pot. energy for each replica separately.. -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: REMD analysis
What do you not like in your distributions? What are your looking for in these distributions? I am not sure what you are expecting from the list here … your distributions are fine, but, as Mark noted, it does not mean your simulation and sampling will be optimal … On May 17, 2013, at 3:51 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, I tried plotting the PE overlap using the following way :- 1. extract PE of each replica using g_energy 2. get the PE distribution using g_analyze -f potential_0.xvg -dist pot0.xvg 3. used xmgrace to plot all the PE distribution graphs together. The same thing I did for temperature distribution for each replica. Here's the file for both PE overlap ( https://www.dropbox.com/s/895f1bi0hkuy884/pe_dist.png) temp distribution (https://www.dropbox.com/s/ed66uop16blgqwa/temp_dist.png) Is this the correct way ?? But the plot doesnot look like this ( https://www.dropbox.com/s/fsuabkl7zrydnib/sample%20PE%20overlap.jpg). Do i have to normalize the data and then plot in order to get a smooth plot like this one?? Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [Spam:*****] [gmx-users] REMD analysis
An acceptance ratio of 0.2/0.3 is normally best. The problem with high acceptance ratio is that it means that a large portion of the exchanges are just back and forth exchanges between consecutive exchange and are thus disturbing the system more that actually helping sampling. I do not know particularly the paper you mention but if you like what they do, it is your choice at the end. Why don;t you just increase the spacing between the replicas? You will need less replicas and potentially you could run two simulations instead of one and evaluate the convergence ... On May 16, 2013, at 1:50 AM, bharat gupta bharat.85.m...@gmail.com wrote: The plots that I showed in my last mail were for all replicas. I tried plotting the first 500 ps of replica_index and replica_time files. I think the plots look fine, and there could be problem with the plotting tool . Here the link for both files , https://www.dropbox.com/s/2g16mlxfsme4rx2/replica_temp.bmp https://www.dropbox.com/s/8jfs0b9whu6j7lo/replica_index.bmp Now regarding the high acceptance ratio which is 0.5 , I came across a paper (http://www.pnas.org/content/100/13/7587.full.pdf), here they have mentioned that their average acceptance ratio ranged between 30 to 80%. I have a question here, how did they calculate the range for the average acceptance ratio or is it average ratio for each replica . Actually, this is the reference I am following. I am also interested in peptide folding simulation, similar to this article. I want to know, whether the average acceptance ratio that I have got for my trial simulation is correct , together with the replica_temp and replica_remd plots. Can I proceed for large production runs to complete my experiment ?? On Tue, May 14, 2013 at 6:34 PM, XAvier Periole x.peri...@rug.nl wrote: The interval between the exchange trial affect the efficiency of REMD but not the the exchange ratio (at least in principle). In you case I am not sure what the plot are showing! Are these showing all the replicas? what are the units? On May 14, 2013, at 5:07 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the result for the REMD trial with large temperature gaps. Temp. distribution : 280.0 294.9 310.7 327.3 344.7 363.1 382.5 402.9 424.4 447.1 471.0 496.1 522.6 550.5 579.9 610.8 Out of md16.log : Replica exchange statistics Repl 249 attempts, 125 odd, 124 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .38 .43 .43 .36 .45 .40 .37 .48 .47 .45 .47 .44 .46 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl 50 42 46 52 57 40 58 49 42 53 61 63 56 57 58 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .37 .42 .46 .32 .46 .40 .34 .43 .49 .51 .45 .46 .46 Average acceptance ratio : 0.46 But, the repli_index.xvg and replica_temp.xvg files still shows that the replicas does not exchange equally well . https://www.dropbox.com/s/zkbwpuj7l2o282b/replica_index.png https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png what could be wrong in this case?? Is it the mdp file settings or implicit solvent setting. Does the time to replica to exhange also affects their swapping ?? On Tue, May 14, 2013 at 12:24 AM, XAvier Periole x.peri...@rug.nl wrote: You need to increase the temperature gaps indeed if you want acceptance ratio ~0.2/0.3. But again this won't work with the water … It is not clear what happens in your index file but probably a problem from grace to plot so many points … you can try to increase the Max drawing path length in the preference menu of grace. On May 13, 2013, at 4:22 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, I repeated the simulation again for 25 replicas with the following temp. distribution . 280 289.1 298.5 308.2 318.2 328.6 339.3 350.3 361.7 373.5 385.6 398.1 411.1 424.4 438.3 452.5 467.2 482.4 498.1 514.3 531.0 548.3 566.1 584.5 603.5 623.2 The output of md.log file is :- Replica exchange statistics Repl 24999 attempts, 12500 odd, 12499 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl .63 .63 .62 .62 .61 .61 .60 .60 .59 .59 .58 .59 .59 .60 .60 .61 .62 .62 .63 .64 .64 .65 .65 .66 .66 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl 7822 7752 7816 7760 7639 7628 7511 7442 7375 7332 7312 7424 7408 7410 7522 7559 7684 7697 7878 7927 7917 8073 8151 8208 8266
Re: [Spam:*****] [gmx-users] REMD analysis
You have to convince yourself, not me :)) But I can give you my opinion … On May 16, 2013, at 10:33 AM, bharat gupta bharat.85.m...@gmail.com wrote: Okay Sir, I will try two-three combinations this time and will report back to you ... On Thu, May 16, 2013 at 5:25 PM, XAvier Periole x.peri...@rug.nl wrote: An acceptance ratio of 0.2/0.3 is normally best. The problem with high acceptance ratio is that it means that a large portion of the exchanges are just back and forth exchanges between consecutive exchange and are thus disturbing the system more that actually helping sampling. I do not know particularly the paper you mention but if you like what they do, it is your choice at the end. Why don;t you just increase the spacing between the replicas? You will need less replicas and potentially you could run two simulations instead of one and evaluate the convergence ... On May 16, 2013, at 1:50 AM, bharat gupta bharat.85.m...@gmail.com wrote: The plots that I showed in my last mail were for all replicas. I tried plotting the first 500 ps of replica_index and replica_time files. I think the plots look fine, and there could be problem with the plotting tool . Here the link for both files , https://www.dropbox.com/s/2g16mlxfsme4rx2/replica_temp.bmp https://www.dropbox.com/s/8jfs0b9whu6j7lo/replica_index.bmp Now regarding the high acceptance ratio which is 0.5 , I came across a paper (http://www.pnas.org/content/100/13/7587.full.pdf), here they have mentioned that their average acceptance ratio ranged between 30 to 80%. I have a question here, how did they calculate the range for the average acceptance ratio or is it average ratio for each replica . Actually, this is the reference I am following. I am also interested in peptide folding simulation, similar to this article. I want to know, whether the average acceptance ratio that I have got for my trial simulation is correct , together with the replica_temp and replica_remd plots. Can I proceed for large production runs to complete my experiment ?? On Tue, May 14, 2013 at 6:34 PM, XAvier Periole x.peri...@rug.nl wrote: The interval between the exchange trial affect the efficiency of REMD but not the the exchange ratio (at least in principle). In you case I am not sure what the plot are showing! Are these showing all the replicas? what are the units? On May 14, 2013, at 5:07 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the result for the REMD trial with large temperature gaps. Temp. distribution : 280.0 294.9 310.7 327.3 344.7 363.1 382.5 402.9 424.4 447.1 471.0 496.1 522.6 550.5 579.9 610.8 Out of md16.log : Replica exchange statistics Repl 249 attempts, 125 odd, 124 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .38 .43 .43 .36 .45 .40 .37 .48 .47 .45 .47 .44 .46 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl 50 42 46 52 57 40 58 49 42 53 61 63 56 57 58 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .37 .42 .46 .32 .46 .40 .34 .43 .49 .51 .45 .46 .46 Average acceptance ratio : 0.46 But, the repli_index.xvg and replica_temp.xvg files still shows that the replicas does not exchange equally well . https://www.dropbox.com/s/zkbwpuj7l2o282b/replica_index.png https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png what could be wrong in this case?? Is it the mdp file settings or implicit solvent setting. Does the time to replica to exhange also affects their swapping ?? On Tue, May 14, 2013 at 12:24 AM, XAvier Periole x.peri...@rug.nl wrote: You need to increase the temperature gaps indeed if you want acceptance ratio ~0.2/0.3. But again this won't work with the water … It is not clear what happens in your index file but probably a problem from grace to plot so many points … you can try to increase the Max drawing path length in the preference menu of grace. On May 13, 2013, at 4:22 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, I repeated the simulation again for 25 replicas with the following temp. distribution . 280 289.1 298.5 308.2 318.2 328.6 339.3 350.3 361.7 373.5 385.6 398.1 411.1 424.4 438.3 452.5 467.2 482.4 498.1 514.3 531.0 548.3 566.1 584.5 603.5 623.2 The output of md.log file is :- Replica exchange statistics Repl 24999 attempts, 12500 odd, 12499 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl .63 .63 .62 .62 .61 .61 .60 .60 .59 .59 .58 .59 .59 .60 .60 .61 .62 .62 .63
Re: [gmx-users] REMD analysis
Indeed the Repeat-3 seems good. But I would guess you did not run too long, right! That would explain the distribution of values! On May 16, 2013, at 2:04 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the result of three different runs : Temperature distribution for three trials Repeat-1 280 298 317 337 359 382 406 432 460 489 520 554 589 627 Repeat-2 280 299 319 340 363 388 414 441 471 503 536 572 611 Repeat-3 280 300 322 345 370 397 426 457 490 526 564 605 649 md.log files output from three different trials: Repeat-1 .37 .28 .26 .30 .25 .29 .32 .35 .32 .35 .36 .32 .31 Repeat-2 .30 .33 .30 .25 .19 .27 .30 .31 .27 .40 .34 .31 Repeat-3 .18 .22 .26 .34 .26 .28 .25 .27 .27 .25 .27 .22 I think as the required acceptance value all the three trials are fine, but trail 3 would be much better to continue the further runs and anlysis ?? So, is it fine to continue with the third simulation ?? But still the problem is that I am not getting the exact graphs with xmgrace?? On Thu, May 16, 2013 at 5:36 PM, XAvier Periole x.peri...@rug.nl wrote: You have to convince yourself, not me :)) But I can give you my opinion … On May 16, 2013, at 10:33 AM, bharat gupta bharat.85.m...@gmail.com wrote: Okay Sir, I will try two-three combinations this time and will report back to you ... On Thu, May 16, 2013 at 5:25 PM, XAvier Periole x.peri...@rug.nl wrote: An acceptance ratio of 0.2/0.3 is normally best. The problem with high acceptance ratio is that it means that a large portion of the exchanges are just back and forth exchanges between consecutive exchange and are thus disturbing the system more that actually helping sampling. I do not know particularly the paper you mention but if you like what they do, it is your choice at the end. Why don;t you just increase the spacing between the replicas? You will need less replicas and potentially you could run two simulations instead of one and evaluate the convergence ... On May 16, 2013, at 1:50 AM, bharat gupta bharat.85.m...@gmail.com wrote: The plots that I showed in my last mail were for all replicas. I tried plotting the first 500 ps of replica_index and replica_time files. I think the plots look fine, and there could be problem with the plotting tool . Here the link for both files , https://www.dropbox.com/s/2g16mlxfsme4rx2/replica_temp.bmp https://www.dropbox.com/s/8jfs0b9whu6j7lo/replica_index.bmp Now regarding the high acceptance ratio which is 0.5 , I came across a paper (http://www.pnas.org/content/100/13/7587.full.pdf), here they have mentioned that their average acceptance ratio ranged between 30 to 80%. I have a question here, how did they calculate the range for the average acceptance ratio or is it average ratio for each replica . Actually, this is the reference I am following. I am also interested in peptide folding simulation, similar to this article. I want to know, whether the average acceptance ratio that I have got for my trial simulation is correct , together with the replica_temp and replica_remd plots. Can I proceed for large production runs to complete my experiment ?? On Tue, May 14, 2013 at 6:34 PM, XAvier Periole x.peri...@rug.nl wrote: The interval between the exchange trial affect the efficiency of REMD but not the the exchange ratio (at least in principle). In you case I am not sure what the plot are showing! Are these showing all the replicas? what are the units? On May 14, 2013, at 5:07 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the result for the REMD trial with large temperature gaps. Temp. distribution : 280.0 294.9 310.7 327.3 344.7 363.1 382.5 402.9 424.4 447.1 471.0 496.1 522.6 550.5 579.9 610.8 Out of md16.log : Replica exchange statistics Repl 249 attempts, 125 odd, 124 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .38 .43 .43 .36 .45 .40 .37 .48 .47 .45 .47 .44 .46 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl 50 42 46 52 57 40 58 49 42 53 61 63 56 57 58 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .37 .42 .46 .32 .46 .40 .34 .43 .49 .51 .45 .46 .46 Average acceptance ratio : 0.46 But, the repli_index.xvg and replica_temp.xvg files still shows that the replicas does not exchange equally well . https://www.dropbox.com/s/zkbwpuj7l2o282b/replica_index.png https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png what could be wrong in this case?? Is it the mdp file settings or implicit solvent setting. Does the time to replica to exhange also affects their swapping
Re: [gmx-users] point in source code to access atom position
Do you need it in the code? g_traj would help you do that on the trajectory. On May 17, 2013, at 3:17 AM, Sikandar Mashayak symasha...@gmail.com wrote: Hi I want to store Z coordinates of atoms at the beginning of each time step when I am doing 'mdrun -rerun'. I am not able to find the line and file in the source code where I can implement this. Can anyone please help me with that? Thanks Sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Large number of solvent molecules
Well, a linear 80aa peptide will need that much water anyways!
The question is more how relevant and realistic is such a structure and how
long the peptide is going to keep it? You could resolvate it after some time,
reducing the box, you could also start by a vacuo simulation to help colapse
your peptide.
But the chance to actually observe folding of such a peptide from a single MD
simulation is about zero. Even using enhance sampling the chance is about zero
unless you get some large access to supercomputers. See DE Shaw papers on
folding.
On May 14, 2013, at 9:44, Erik Marklund er...@xray.bmc.uu.se wrote:
Hi,
Have a look at the following article. It describes a non-standard box type
that seems ideal for your application. I don't know what is the latest
gromacs version where it is implemented, however.
Author = {Wassenaar, TA and Mark, AE},
Title = {{The effect of box shape on the dynamic properties of proteins
simulated
under periodic boundary conditions}},
Journal = {{JOURNAL OF COMPUTATIONAL CHEMISTRY}},
Year = {{2006}},
Volume = {{27}},
Number = {{3}},
Pages = {{316-325}},
On 14 May 2013, at 07:44, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote:
Thank you Dr. Dallas. Yes I think the issue is that the starting
conformation is linear, as I want to study its folding properties. I tried
the same with helical starting conformation, and got around 11 water
molecules, which is still ok.
I am trying to find a way to simulate a 89 aa peptide in linear starting
conformation such that the simulation is practically feasible.
On Tue, May 14, 2013 at 10:45 AM, Dallas Warren
dallas.war...@monash.eduwrote:
From the box volume printed in the script output it appears you have a
box that is approximately a 28nm cube. And that size box requires a
significant number of water molecules to fill up, so that number you have
in there (~770,000) seems about correct.
If you want to have less water molecules, then you will need to make the
simulation cell smaller. Whether that is possible or not depends on what
you are looking to observe, how big the molecule you are solvating is etc.
Catch ya,
Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a
nail.
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
boun...@gromacs.org] On Behalf Of Nikunj Maheshwari
Sent: Tuesday, 14 May 2013 3:04 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] Large number of solvent molecules
Dear all,
I am trying to see the folding of a 89 aa peptide. So I am setting up
the
system from linear conformation.
I gave the following commands to build the box and add the solvent
molecules.
editconf -f output.gro -c -d 1.0 -bt dodecahedron -o outbox.gro
genbox -cp outbox.gro -cs spc216.gro -p topol.top -o outh2o.gro
Reading solute configuration
Go Rough, Oppose Many Angry Chinese Serial killers
Containing 1440 atoms in 89 residues
Initialising van der waals distances...
WARNING: Masses and atomic (Van der Waals) radii will be guessed
based on residue and atom names, since they could not be
definitively assigned from the information in your input
files. These guessed numbers might deviate from the mass
and radius of the atom type. Please check the output
files if necessary.
Reading solvent configuration
216H2O,WATJP01,SPC216,SPC-
MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984
solvent configuration contains 648 atoms in 216 residues
Initialising van der waals distances...
Will generate new solvent configuration of 18x18x13 boxes
Generating configuration
Sorting configuration
Found 1 molecule type:
SOL ( 3 atoms): 909792 residues
Calculating Overlap...
box_margin = 0.315
Removed 324522 atoms that were outside the box
Neighborsearching with a cut-off of 0.48
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's: NS: 0.48 Coulomb: 0.48 LJ: 0.48
System total charge: 0.000
Grid: 73 x 73 x 51 cells
Successfully made neighbourlist
nri = 3007232, nrj = 82473964
Checking Protein-Solvent overlap: tested 36005 pairs, removed 1653
atoms.
Checking Solvent-Solvent overlap: tested 7152003 pairs, removed 73182
atoms.
Added 776673 molecules
Generated solvent containing 2330019 atoms in 776673 residues
Writing generated configuration to outh2o.gro
Back Off! I just backed up outh2o.gro to ./#outh2o.gro.1#
Go Rough, Oppose Many Angry Chinese Serial killers
Output configuration contains 2331459 atoms in 776762 residues
Volume : 23276.3 (nm^3)
Density: 1001.32 (g/l)
Number of SOL molecules: 776673
Processing topology
Re: [Spam:*****] [gmx-users] REMD analysis
The interval between the exchange trial affect the efficiency of REMD but not the the exchange ratio (at least in principle). In you case I am not sure what the plot are showing! Are these showing all the replicas? what are the units? On May 14, 2013, at 5:07 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the result for the REMD trial with large temperature gaps. Temp. distribution : 280.0 294.9 310.7 327.3 344.7 363.1 382.5 402.9 424.4 447.1 471.0 496.1 522.6 550.5 579.9 610.8 Out of md16.log : Replica exchange statistics Repl 249 attempts, 125 odd, 124 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .38 .43 .43 .36 .45 .40 .37 .48 .47 .45 .47 .44 .46 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl 50 42 46 52 57 40 58 49 42 53 61 63 56 57 58 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .37 .42 .46 .32 .46 .40 .34 .43 .49 .51 .45 .46 .46 Average acceptance ratio : 0.46 But, the repli_index.xvg and replica_temp.xvg files still shows that the replicas does not exchange equally well . https://www.dropbox.com/s/zkbwpuj7l2o282b/replica_index.png https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png what could be wrong in this case?? Is it the mdp file settings or implicit solvent setting. Does the time to replica to exhange also affects their swapping ?? On Tue, May 14, 2013 at 12:24 AM, XAvier Periole x.peri...@rug.nl wrote: You need to increase the temperature gaps indeed if you want acceptance ratio ~0.2/0.3. But again this won't work with the water … It is not clear what happens in your index file but probably a problem from grace to plot so many points … you can try to increase the Max drawing path length in the preference menu of grace. On May 13, 2013, at 4:22 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, I repeated the simulation again for 25 replicas with the following temp. distribution . 280 289.1 298.5 308.2 318.2 328.6 339.3 350.3 361.7 373.5 385.6 398.1 411.1 424.4 438.3 452.5 467.2 482.4 498.1 514.3 531.0 548.3 566.1 584.5 603.5 623.2 The output of md.log file is :- Replica exchange statistics Repl 24999 attempts, 12500 odd, 12499 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl .63 .63 .62 .62 .61 .61 .60 .60 .59 .59 .58 .59 .59 .60 .60 .61 .62 .62 .63 .64 .64 .65 .65 .66 .66 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl 7822 7752 7816 7760 7639 7628 7511 7442 7375 7332 7312 7424 7408 7410 7522 7559 7684 7697 7878 7927 7917 8073 8151 8208 8266 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl .63 .62 .63 .62 .61 .61 .60 .60 .59 .59 .58 .59 .59 .59 .60 .60 .61 .62 .63 .63 .63 .65 .65 .66 .66 The average acceptance ration is around 0.6 which is still high. The link for replica_temp,replica_index : https://www.dropbox.com/s/c7soajnwc3uww8j/replica_temp.png https://www.dropbox.com/s/wvx82m4c6cnsfit/replica_index.png The temp files look better but the index file looks weird ... Do i need to experiment with the gap difference in order to get the required ration of 0.2-0.3 ?? There is some problem with the .mdp file settings?? -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use
Re: [gmx-users] Issue running gromacs in Cluster
You may have created large files and thus got out of quota on the disc. Check your quota and consider reducing the frequency of saving coordinates. On May 13, 2013, at 9:46, Sainitin Donakonda saigr...@gmail.com wrote: Hello, I am trying to run 20 ns protein ligand simulation on cluster using following MD.MDP file ; 7.3.3 Run Control integrator = md; leap-frog integrator dt = 0.002 ; 2 fs nsteps = 500; maximum number of steps to integrate ; 7.3.8 Output Control nstxout = 200 ; suppress .trr output nstvout = 200; suppress .trr output nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps nstxtcout = 1000 ; write .xtc trajectory every 2 ps energygrps = Protein LIG ; 7.3.9 Neighbor Searching nstlist = 5 ; [steps] freq to update neighbor list ns_type = grid ; method of updating neighbor list pbc = xyz ; periodic boundary conditions in all directions rlist = 1.2 ; [nm] cut-off distance for the short-range neighbor list ; 7.3.10 Electrostatics coulombtype = PME ; Particle-Mesh Ewald electrostatics rcoulomb= 1.2 ; [nm] distance for Coulomb cut-off ; 7.3.11 VdW vdwtype = switch ; twin-range cut-off with rlist where rvdw = rlist rvdw= 1.2 ; [nm] distance for LJ cut-off rvdw_switch = 0.8 ; Start switching th LJ potential DispCorr= EnerPres ; apply long range dispersion corrections for energy ; 7.3.13 Ewald fourierspacing = 0.12 ; [nm] grid spacing for FFT grid when using PME pme_order = 4 ; interpolation order for PME, 4 = cubic ewald_rtol = 1e-5 ; relative strength of Ewald-shifted potential at rcoulomb ; 7.3.14 Temperature Coupling tcoupl = V-rescale ; temperature coupling with Berendsen-thermostat tc_grps = Protein_LIG Water_and_ions; groups to couple seperately to temperature bath tau_t = 0.10.1; [ps] time constant for coupling ref_t = 300300; [K] reference temperature for coupling ; Pressure coupling pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 refcoord_scaling= com ; 7.3.17 Velocity Generation gen_vel = no; velocity generation turned off ; 7.3.18 Bonds constraints = all-bonds ; convert all bonds to constraints constraint_algorithm= LINCS ; LINear Constraint Solver continuation= yes ; apply constraints to the start configuration lincs_order = 4 ; highest order in the expansion of the contraint coupling matrix lincs_iter = 1 ; number of iterations to correct for rotational lengthening lincs_warnangle = 30; [degrees] maximum angle that a bond can rotate before LINCS will complain *and im using following commands dividing 20 ns to 10 ns each via extending simulation* *#This is the first simulation MD.mdp file contains 20 ns setup* grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o MD_first10.tpr mpirun -n 16 mdrun -s MD_first10.tpr -deffnm MD_first10 -np 16 *#This extends 10 ns simulation* tpbconv -s MD_first10.tpr -extend 1 -o md_extended.tpr mpirun -n 16 mdrun -s md_extended.tpr -deffnm MD_first10 -cpi MD_first10.cpt -append -np 16 But it is crashed giving following error *XTC error - maybe you are out of quota?* * * *dont know why it happened it is because as im saving .trr file every 200ps? is it creating large files? or should i give different name in extending simulation?* * * *Please help* * * *Thanks,* *Nitin* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search
Re: [gmx-users] issue in replica exchange
Ok, the redmine is filled up and anybody who has time to help finding the issue is welcome :) I can't do much more! As an alternative a colleague suggested that I could potentially get around the problem by using a compilation combining Open-MP or thread-MPI for each replica running on one node (shared memory=no need of decomposition) and MPI across nodes. Would it work? But I might have a problem, the CG uses shifted potentials and they seem not to be implemented with OpenMP and thread-MPI is not compatible with MPI … Any other solution one could imagine? XAvier. On May 9, 2013, at 1:01 PM, XAvier Periole x.peri...@rug.nl wrote: I finally could reproduce the problem in gmx461 and have fled up a red mine report. I hope we can fix this easily but I am not sure how things go go from now! Someone will get the bug assigned and fix it when ever possible or something else? Thank you all for the help, XAvier. On May 2, 2013, at 10:15 PM, XAvier Periole x.peri...@rug.nl wrote: I'll look at the 4.6.1 version next week, I could install it but I got a conflict between the environmental variable defining openMP variable but I turned it off during compilation … You could try to run on particle decomposition to see if you get a problem … it should one quite quick. On May 2, 2013, at 2:36 PM, Michael Shirts mrshi...@gmail.com wrote: Both. So if 4.6.1 doesn't work, I want to know so we can patch it before 4.6.2 comes out. If it does work, then there is probably stuff that can be backported. On Thu, May 2, 2013 at 8:32 AM, XAvier Periole x.peri...@rug.nl wrote: You mean working with or working on the code? I'll try gmx-4.6.1 On May 2, 2013, at 2:26 PM, Michael Shirts mrshi...@gmail.com wrote: Quick check here -- is 4.6 behaving correctly? I actually spent some time working on REMD in 4.6, and it seems to be behaving correctly in my hands with temperature and pressure control. Thanks for any additional info on this! On Thu, May 2, 2013 at 8:18 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Thu, May 2, 2013 at 12:58 PM, XAvier Periole x.peri...@rug.nl wrote: I saw that redmine report, which could be related but it seems to happen only for runs done outside the domain and particle decompositions. I'll fill up a red mine. Anything I could do to help speeding the fix? What'd be really nice is some thought on how one can demonstrate that the implementation of the exchange matches what would be expected from the theory. For T-exchange under NVT, it is sufficient to rescale velocities and quantities derived from them by the correct factor. That includes various things like T-coupling history and integrator half-step quantities (and does REMD with leap-frog make sense anyway?). For NPT, there's probably also some P-coupling quantities to scale, and the box to exchange. Anything I've missed? Hopefully virial contributions don't matter either way? Perhaps a decent first step is to hack the code to do a self exchange, by clearing the entire state and rebuilding with what would/should be received from an exchange with a hypothethetical replica in an identical pre-exchange state. Only if the code can do that (i.e. mdrun -reprod produces a trajectory indistinguishable from a run that does not attempt this self exchange) is it worth considering proper state exchanges, and the process of making the code do the former should illustrate what is required for the latter. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests
Re: [Spam:*****] [gmx-users] REMD analysis
You need to increase the temperature gaps indeed if you want acceptance ratio ~0.2/0.3. But again this won't work with the water … It is not clear what happens in your index file but probably a problem from grace to plot so many points … you can try to increase the Max drawing path length in the preference menu of grace. On May 13, 2013, at 4:22 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, I repeated the simulation again for 25 replicas with the following temp. distribution . 280 289.1 298.5 308.2 318.2 328.6 339.3 350.3 361.7 373.5 385.6 398.1 411.1 424.4 438.3 452.5 467.2 482.4 498.1 514.3 531.0 548.3 566.1 584.5 603.5 623.2 The output of md.log file is :- Replica exchange statistics Repl 24999 attempts, 12500 odd, 12499 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl .63 .63 .62 .62 .61 .61 .60 .60 .59 .59 .58 .59 .59 .60 .60 .61 .62 .62 .63 .64 .64 .65 .65 .66 .66 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl 7822 7752 7816 7760 7639 7628 7511 7442 7375 7332 7312 7424 7408 7410 7522 7559 7684 7697 7878 7927 7917 8073 8151 8208 8266 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl .63 .62 .63 .62 .61 .61 .60 .60 .59 .59 .58 .59 .59 .59 .60 .60 .61 .62 .63 .63 .63 .65 .65 .66 .66 The average acceptance ration is around 0.6 which is still high. The link for replica_temp,replica_index : https://www.dropbox.com/s/c7soajnwc3uww8j/replica_temp.png https://www.dropbox.com/s/wvx82m4c6cnsfit/replica_index.png The temp files look better but the index file looks weird ... Do i need to experiment with the gap difference in order to get the required ration of 0.2-0.3 ?? There is some problem with the .mdp file settings?? -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] REMD average acceptance ratio
Well, actually things do not look so good. But is it possible that grace is actually no able to plot things correctly? You have line going throughout the plot from complete-left to complete-right! I am do not know what the t-rems calculator does but apparently it is not optimal in your case. Did you try to use the simple rule Tn=T0 x exp(n c), where T0 is close to your starting temperature and c is a constant that you can tune and will define the spacing between the temperatures. From your current data you can guess the spacing and thus the c value you need. Note that the exchange ratio is quickly converging in the simulation so you can make a few trials … On May 11, 2013, at 1:40 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Thank you for your reply. I choose the temperature distribution using t-remd calculator. Here's the link for index and temp files . https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m. On Sat, May 11, 2013 at 12:04 AM, XAvier Periole x.peri...@rug.nl wrote: The replicas seem indeed to have exchange. Using a colour for the # replicas would help. I could not access to the first link. Note also that the increase of exchange ratio with the temperature suggest the distribution of the temperature is not optimal and may be with regular intervals? You want to use a exponential distribution. On May 10, 2013, at 4:53 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear gmx members, I have posted the same question previously , but I didn't get any reply. So, if anyone can help me out ... I performed a REMD simulation on a peptide 384 atoms (24 residues). In total 11 replicas were simulated for a period of 50ns each. The exchange was allwoed at every 1000 steps. The output of md.log file is : Replica exchange statistics Repl 24999 attempts, 12500 odd, 12499 even Repl average probabilities: Repl 0123456789 10 Repl .16 .16 .16 .17 .18 .21 .24 .26 .28 .30 Repl number of exchanges: Repl 0123456789 10 Repl 2038 2007 2065 2117 2182 2587 3022 3213 3554 3703 Repl average number of exchanges: Repl 0123456789 10 Repl .16 .16 .17 .17 .17 .21 .24 .26 .28 .30 The acceptance ratio for each replica and average acceptance ratio is as calculated below :- accp. ratio 2038 0.16304 2007 0.16056 2065 0.1652 2117 0.16936 2182 0.17456 2587 0.20696 3022 0.24176 3213 0.25704 3554 0.28432 3703 0.29624 0.211904 (avg accp ratio) (Is this value correct ??) The Pdes used while generating temp. range was also 0.2. Does that mean that replicas have exchanged for the given temp.range ??. Here's the link for both remd_temp and remd_index files ( https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png;cid=1368069857486-810 ) , ( https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?mcid=1368069857486-810 ) -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Biomolecular Engineering Laboratory Pusan National University South Korea Mobile no. - 010-5818-3680 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] REMD average acceptance ratio
You are simulating in vacuo! Otherwise the temperature gaps are way too large … If you want to analyse the sampling at 300 K, I would suggest you start you first temperature lower, around 280/285 may be. At least to have your second temperature at 300 K. the value of c has absolutely not importance … the temperature distribution has … make some test to see how the acceptance ratio evolves … On May 11, 2013, at 5:05 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the temperature range that I got form t-remd : 1 300 2 323.7 3 348.75 4 375.23 5 403.22 6 432.83 7 464.14 8 497.24 9 532.26 10 569.32 11 608.51 according the above equation c should be somewhere around 2.37. On Sat, May 11, 2013 at 11:10 PM, XAvier Periole x.peri...@rug.nl wrote: Well, actually things do not look so good. But is it possible that grace is actually no able to plot things correctly? You have line going throughout the plot from complete-left to complete-right! I am do not know what the t-rems calculator does but apparently it is not optimal in your case. Did you try to use the simple rule Tn=T0 x exp(n c), where T0 is close to your starting temperature and c is a constant that you can tune and will define the spacing between the temperatures. From your current data you can guess the spacing and thus the c value you need. Note that the exchange ratio is quickly converging in the simulation so you can make a few trials … On May 11, 2013, at 1:40 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Thank you for your reply. I choose the temperature distribution using t-remd calculator. Here's the link for index and temp files . https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m. On Sat, May 11, 2013 at 12:04 AM, XAvier Periole x.peri...@rug.nl wrote: The replicas seem indeed to have exchange. Using a colour for the # replicas would help. I could not access to the first link. Note also that the increase of exchange ratio with the temperature suggest the distribution of the temperature is not optimal and may be with regular intervals? You want to use a exponential distribution. On May 10, 2013, at 4:53 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear gmx members, I have posted the same question previously , but I didn't get any reply. So, if anyone can help me out ... I performed a REMD simulation on a peptide 384 atoms (24 residues). In total 11 replicas were simulated for a period of 50ns each. The exchange was allwoed at every 1000 steps. The output of md.log file is : Replica exchange statistics Repl 24999 attempts, 12500 odd, 12499 even Repl average probabilities: Repl 0123456789 10 Repl .16 .16 .16 .17 .18 .21 .24 .26 .28 .30 Repl number of exchanges: Repl 0123456789 10 Repl 2038 2007 2065 2117 2182 2587 3022 3213 3554 3703 Repl average number of exchanges: Repl 0123456789 10 Repl .16 .16 .17 .17 .17 .21 .24 .26 .28 .30 The acceptance ratio for each replica and average acceptance ratio is as calculated below :- accp. ratio 2038 0.16304 2007 0.16056 2065 0.1652 2117 0.16936 2182 0.17456 2587 0.20696 3022 0.24176 3213 0.25704 3554 0.28432 3703 0.29624 0.211904 (avg accp ratio) (Is this value correct ??) The Pdes used while generating temp. range was also 0.2. Does that mean that replicas have exchanged for the given temp.range ??. Here's the link for both remd_temp and remd_index files ( https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png;cid=1368069857486-810 ) , ( https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?mcid=1368069857486-810 ) -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Biomolecular Engineering Laboratory Pusan National University South Korea Mobile no. - 010-5818-3680 -- gmx
Re: [gmx-users] REMD average acceptance ratio
The values of exchange ratio look much better: they are similar over the range of temperatures. To reduce the ratio you have to increase the spacing between temperatures, which means increase the value of c in the formula I gave earlier. When you but the water in, the degrees of freedom (and thus the potential energy) will increase and the temperature distribution won't work at all! To cover the same temperature range you'll need much more temperatures. On May 11, 2013, at 19:59, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, I tried again with the following temp. ditribution, this time with 30 replicas (280 K -624K) and 500 ps simulation time for each one. 0 280 1 287.8 2 295.9 3 304.2 4 312.7 5 321.5 6 330.5 7 339.8 8 349.3 9 359.1 10 369.1 11 379.5 12 390.1 13 401.0 14 412.3 15 423.8 16 435.7 17 447.9 18 460.4 19 473.3 20 486.6 21 500.2 22 514.3 23 528.7 24 543.5 25 558.7 26 574.4 27 590.4 28 607.0 29 624.0 The output of md29.log file is :- Replica exchange statistics Repl 249 attempts, 125 odd, 124 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 Repl .68 .63 .62 .68 .71 .66 .69 .68 .71 .67 .64 .71 .69 .71 .66 .69 .73 .73 .72 .73 .69 .71 .71 .74 .73 .70 .72 .74 .71 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 Repl 81 77 79 90 93 78 91 80 88 78 81 92 96 94 81 83 90 92 83 97 89 87 91 94 88 84 85 89 86 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 Repl .65 .62 .63 .73 .74 .63 .73 .65 .70 .63 .65 .74 .77 .76 .65 .67 .72 .74 .66 .78 .71 .70 .73 .76 .70 .68 .68 .72 .69 The average acceptance ration comes around 0.69 , which is very high. Now, in order to get the avg. acceptance ration between 0.2 to 0.3 and also all the replicas should exchange , what has to be done. Here's the link for remd_index and remd_temp files https://www.dropbox.com/s/sgpblcdg9zh7f52/remd_temp.png https://www.dropbox.com/s/6hvqlqmu64mb2jy/remd_index.png I want to that if I include water for the simulation, the same temp. distribution would work or not ?? On Sun, May 12, 2013 at 12:10 AM, XAvier Periole x.peri...@rug.nl wrote: You are simulating in vacuo! Otherwise the temperature gaps are way too large … If you want to analyse the sampling at 300 K, I would suggest you start you first temperature lower, around 280/285 may be. At least to have your second temperature at 300 K. the value of c has absolutely not importance … the temperature distribution has … make some test to see how the acceptance ratio evolves … On May 11, 2013, at 5:05 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the temperature range that I got form t-remd : 1 300 2 323.7 3 348.75 4 375.23 5 403.22 6 432.83 7 464.14 8 497.24 9 532.26 10 569.32 11 608.51 according the above equation c should be somewhere around 2.37. On Sat, May 11, 2013 at 11:10 PM, XAvier Periole x.peri...@rug.nl wrote: Well, actually things do not look so good. But is it possible that grace is actually no able to plot things correctly? You have line going throughout the plot from complete-left to complete-right! I am do not know what the t-rems calculator does but apparently it is not optimal in your case. Did you try to use the simple rule Tn=T0 x exp(n c), where T0 is close to your starting temperature and c is a constant that you can tune and will define the spacing between the temperatures. From your current data you can guess the spacing and thus the c value you need. Note that the exchange ratio is quickly converging in the simulation so you can make a few trials … On May 11, 2013, at 1:40 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Thank you for your reply. I choose the temperature distribution using t-remd calculator. Here's the link for index and temp files . https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m. On Sat, May 11, 2013 at 12:04 AM, XAvier Periole x.peri...@rug.nl wrote: The replicas seem indeed to have exchange. Using a colour for the # replicas would help. I could not access to the first link. Note also that the increase of exchange ratio with the temperature suggest the distribution of the temperature is not optimal and may be with regular intervals? You want to use a exponential distribution. On May 10, 2013, at 4:53 PM
Re: [gmx-users] Re: REMD average acceptance ratio
The replicas seem indeed to have exchange. Using a colour for the # replicas would help. I could not access to the first link. Note also that the increase of exchange ratio with the temperature suggest the distribution of the temperature is not optimal and may be with regular intervals? You want to use a exponential distribution. On May 10, 2013, at 4:53 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear gmx members, I have posted the same question previously , but I didn't get any reply. So, if anyone can help me out ... I performed a REMD simulation on a peptide 384 atoms (24 residues). In total 11 replicas were simulated for a period of 50ns each. The exchange was allwoed at every 1000 steps. The output of md.log file is : Replica exchange statistics Repl 24999 attempts, 12500 odd, 12499 even Repl average probabilities: Repl 0123456789 10 Repl .16 .16 .16 .17 .18 .21 .24 .26 .28 .30 Repl number of exchanges: Repl 0123456789 10 Repl 2038 2007 2065 2117 2182 2587 3022 3213 3554 3703 Repl average number of exchanges: Repl 0123456789 10 Repl .16 .16 .17 .17 .17 .21 .24 .26 .28 .30 The acceptance ratio for each replica and average acceptance ratio is as calculated below :- accp. ratio 2038 0.16304 2007 0.16056 2065 0.1652 2117 0.16936 2182 0.17456 2587 0.20696 3022 0.24176 3213 0.25704 3554 0.28432 3703 0.29624 0.211904 (avg accp ratio) (Is this value correct ??) The Pdes used while generating temp. range was also 0.2. Does that mean that replicas have exchanged for the given temp.range ??. Here's the link for both remd_temp and remd_index files ( https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.pnghttps://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png;cid=1368069857486-810) , ( https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?mhttps://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?mcid=1368069857486-810 ) -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] issue in replica exchange
I finally could reproduce the problem in gmx461 and have fled up a red mine report. I hope we can fix this easily but I am not sure how things go go from now! Someone will get the bug assigned and fix it when ever possible or something else? Thank you all for the help, XAvier. On May 2, 2013, at 10:15 PM, XAvier Periole x.peri...@rug.nl wrote: I'll look at the 4.6.1 version next week, I could install it but I got a conflict between the environmental variable defining openMP variable but I turned it off during compilation … You could try to run on particle decomposition to see if you get a problem … it should one quite quick. On May 2, 2013, at 2:36 PM, Michael Shirts mrshi...@gmail.com wrote: Both. So if 4.6.1 doesn't work, I want to know so we can patch it before 4.6.2 comes out. If it does work, then there is probably stuff that can be backported. On Thu, May 2, 2013 at 8:32 AM, XAvier Periole x.peri...@rug.nl wrote: You mean working with or working on the code? I'll try gmx-4.6.1 On May 2, 2013, at 2:26 PM, Michael Shirts mrshi...@gmail.com wrote: Quick check here -- is 4.6 behaving correctly? I actually spent some time working on REMD in 4.6, and it seems to be behaving correctly in my hands with temperature and pressure control. Thanks for any additional info on this! On Thu, May 2, 2013 at 8:18 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Thu, May 2, 2013 at 12:58 PM, XAvier Periole x.peri...@rug.nl wrote: I saw that redmine report, which could be related but it seems to happen only for runs done outside the domain and particle decompositions. I'll fill up a red mine. Anything I could do to help speeding the fix? What'd be really nice is some thought on how one can demonstrate that the implementation of the exchange matches what would be expected from the theory. For T-exchange under NVT, it is sufficient to rescale velocities and quantities derived from them by the correct factor. That includes various things like T-coupling history and integrator half-step quantities (and does REMD with leap-frog make sense anyway?). For NPT, there's probably also some P-coupling quantities to scale, and the box to exchange. Anything I've missed? Hopefully virial contributions don't matter either way? Perhaps a decent first step is to hack the code to do a self exchange, by clearing the entire state and rebuilding with what would/should be received from an exchange with a hypothethetical replica in an identical pre-exchange state. Only if the code can do that (i.e. mdrun -reprod produces a trajectory indistinguishable from a run that does not attempt this self exchange) is it worth considering proper state exchanges, and the process of making the code do the former should illustrate what is required for the latter. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search
Re: [gmx-users] keeping water (entirely) out of the bilayer core
You could define a repulsive potential that would apply to water molecules. I
am not sure how it is called but it is available and described in the manual.
On May 4, 2013, at 2:46, Christopher Neale chris.ne...@mail.utoronto.ca wrote:
Dear users:
I am interested in running simulations of lipid bilayers in which I keep all
water molecules out of the bilayer core
(not just statistically, but absolutely). However, I have been unable to
figure out how to do it.
I'll list what I have tried in the hope that others have some ideas or even
perhaps know how to do this
with standard gromacs.
Everything that I have tried revolves around using the pull code, setting the
entire lipid bilayer as the reference
group, and having thousands of pulled groups -- one for each water molecule.
Also, I modified the gromacs
source code in mdlib/pull.c (version 4.6.1) so that the force is only applied
when the displacement is smaller than
the desired distance and not when the displacement is larger than the
specified distance (to keep water out but
then to otherwise let it go anywhere without bias):
static void do_pull_pot(int ePull,
t_pull *pull, t_pbc *pbc, double t, real lambda,
real *V, tensor vir, real *dVdl)
{
intg, j, m;
dvec dev;
double ndr, invdr;
real k, dkdl;
t_pullgrp *pgrp;
/* loop over the groups that are being pulled */
*V= 0;
*dVdl = 0;
for (g = 1; g 1+pull-ngrp; g++)
{
pgrp = pull-grp[g];
get_pullgrp_distance(pull, pbc, g, t, pgrp-dr, dev);
/* ## HERE IS THE CODE CHANGE
if(dev[0]0.0){
dev[0]=0.0;
}
/* End code snippit */
The most relevant lines from the .mdp file were:
pull = umbrella
pull_geometry= distance
pull_dim = N N Y
pull_start = no
pull_ngroups = 9000
pull_group0 = POPC
pull_group1 = r_1__OW
pull_init1 = 1.9
pull_k1 = 500
pull_group2 = r_2__OW
pull_init2 = 1.9
pull_k2 = 500
... etc...
The problem with this was that it crashed immediately with an error that my
pulling distance was
greater than 1/2 of the box vector.:
Fatal error:
Distance of pull group 165 (5.353939 nm) is larger than 0.49 times the box
size (5.395960)
Pretty obvious in retrospect. If I could get this error to go away, then
everything should be fine because I have modified the code so that forces are
zero at large displacements. However, I am worried that if I simply modify
grompp to bypass this error then I might get some type of strange and
possibly silent error in mdrun. Any thoughts on this are really appreciated.
For my second try, I used pull_geometry = direction-periodic (see more
details below), but that also didn't work
because if I set pull_vec1 = 0 0 1, then everything gets pulled to the upper
part of the box (and LINCS errors
ensue), rather than simply pulling away from the bilayer.
Pcoupl= berendsen
pcoupltype = semiisotropic
compressibility= 4.5e-5 0
pull = umbrella
pull_geometry= direction-periodic
pull_start = no
pull_ngroups = 9000
pull_group0 = POPC
pull_group1 = r_1__OW
pull_init1 = 1.9
pull_k1 = 500
pull_vec1= 0 0 1
pull_group2 = r_2__OW
pull_init2 = 1.9
pull_k2 = 500
pull_vec2= 0 0 1
... etc...
If anybody has an idea about how I could get this to work with standard
gromacs or with a modified version, I would be very grateful to hear your
thoughts.
Thank you,
Chris.
--
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Re: [gmx-users] local pressure
What are you looking for? Have a look at the papers they might be inspiring :)) On May 1, 2013, at 10:33 PM, Sikandar Mashayak symasha...@gmail.com wrote: Ok, I did rerun with local pressure mdrun, and got pressure.dat* files in binary format. how do I proceed from here? Any utility to analyze or post-process this? On Wed, May 1, 2013 at 11:11 AM, Sikandar Mashayak symasha...@gmail.comwrote: Thanks Xavier, I will give it a try. On Wed, May 1, 2013 at 10:56 AM, XAvier Periole x.peri...@rug.nl wrote: Well I am not the expert. O.H.S. Ollila, M. Louhivuori and E. Lindahl are :)). The paper related to the use would be: Ollila et al, PRL 102, 078101 (2009) Ollila et al, Biophysical Journal (100)1651–59 On May 1, 2013, at 5:48 PM, Sikandar Mashayak symasha...@gmail.com wrote: Thanks Xavier Can you please elaborate on how to use and post-process the local pressure version of gromacs? Do you have any examples or reference article? May be you can create a HowTo wiki as Justin suggested, it would be of great help. Thanks Sikandar On Wed, May 1, 2013 at 5:03 AM, Justin Lemkul jalem...@vt.edu wrote: On 5/1/13 5:12 AM, XAvier Periole wrote: The use of the original code is quite straightforward, the post processing is a bit more confusing but quite accessible. That would be a great topic for a wiki How-To. We have been using this code (the one available on the site) and related version in the lab and we definitely would find it very sad to not keep this feature available in GROMACS. I never said it would go away, but given the fact that there have been no updates to the git branch in over 3 years, it's simply unlikely that anyone has cared to move it forward. If someone wants to update the code to be compatible with 4.6, that would be a welcome contribution. Lack of any request for improvements and inclusion in an official release has likely led to the decline in interest from the development team. If you want something included, you should file a feature request on redmine.gromacs.org - it's the only official way we keep track of fixes and features. If it's not there, it likely won't get addressed until one of the developers has a compelling need to work on it. -Justin On May 1, 2013, at 2:34 AM, Justin Lemkul jalem...@vt.edu wrote: On 4/30/13 8:01 PM, Sikandar Mashayak wrote: Hi I found the branch of gromacs code called localpressure-4.0 at http://redmine.gromacs.org/**projects/gromacs/repository/** show?rev=localpressure-4-0 http://redmine.gromacs.org/projects/gromacs/repository/show?rev=localpressure-4-0 . I am wondering whether this code can compute the spatial variation of pressure in given system. And if it does, how stable is this branch? Are there any known issues with it? And any particular reason this is not included in main gromacs releases? Lack of documentation has made it very difficult to use, it is extremely slow, and no one ever asks about it except once every few years. All of those factors make it unlikely to ever incorporate into an actual release. Given that the development process has gone on for years in the absence of any real interest in the localpressure branch, it's probably more trouble than it's worth to get it up and running effectively. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post
Re: [gmx-users] issue in replica exchange
Did you look at some data like temperature/pressure/box size/Epot as a function
of time and especially around some exchanges?
Your system is atomistic I presume.
On May 2, 2013, at 12:38 PM, Simone Conti simone...@gmail.com wrote:
I'm running remd in NPT ensemble for a small peptide and all is ok if the
maximum temperature is below 510/520 kelvin. I use Nosé-Hoover termostat
and Parrinello-Rahman barostat. Ref T from 285 to 500K and ref P equals to
1bar. Gromacs version 4.5.5. Exchange trials every 5 ps.
If I try to add replica at a higher temperature the system crash, but I
think it is a problem of equilibration.
2013/5/1 XAvier Periole x.peri...@rug.nl
Ok here is my current status on that REMD issue.
For info: I use
Temperature: v-rescale, tau_t = 2.0 ps
Pressure: berendsen, tau_p = 5.0 ps,
time step: dt=0.002 - 0.020 fs,
COM removal on for bilayer/water separately
The symptoms: explosion of the system after 2-5 steps following the swap,
first sign is a huge jump in LJ interactions and pressure. This jump seems
to be absorbed by the box size and temperature when possible … see example
I provided earlier. A large VCM (velocity centre of mass?) is often
associated with the crash. But also pressure scaling more than 1% ...
1- the problem mentioned above remains in gmx-4.5.7 and it might actually
got worse. I was able to run a 500 ns simulation with gmx405 using similar
setup as for gmx457. The following point happened in gmx457.
2- it persists with a time step of 2 fs. Actually all tests performed in
the following used dt=2fs.
3- if I perform an exchange that explodes within mdrun myself (externally
to the remd gromacs by getting the gro file with the mdp adjusting the
temperature) it goes all fine.
4- the issue gets much worst when the consecutive replicas differ
(different protein conformations and the box size etc) … explosion at first
exchange.
5- the use of parrinelo-raman does not help
6- cancelling the centre of mass removal does not remove the problem.
7- switching to NVT ensemble does not help but makes it worst (crash in 2
steps). All exchanges accepted at first attempt crash with the message
Large VCM(group SOL): -0.0XXX , -0.XXX, -0.16XXX, Temp-cm:6.55XXX
8- using a unique conformation (the same) for all replicas in the NVT REMD
simulation after equilibration in the same NVT ensemble (for 1 ns) removes
the problem.
9- taking the equilibrated NVT conformations, equilibrate them in an NPT
ensemble (1 ns) and let go the exchanges afterwards restores the problem …
one exchange is not properly done at the second trial, while the first ones
were fine. Well if errors were made that was with reasonable
10- note also that the coarse grain I use is extremely forgiving, meaning
you can perform really nasty transformations and run it further after
simple minimisation … so even abrupt changes in temperatures should be fine
and relax quickly.
11- when looking at the conformations themselves nothing appears to have
jumped over or nothing funky.
At this point I am not sure what to think and what to do next. There is
definitely something not going right during the exchanges.
Anyone has been able to run a REMD simulation in an NPT ensemble without
crashes? I would imagine someone has and something particular to my system
is making it going wrong but I am really wondering what it could be. My
feeling is that something relative to the box size or pressure is not going
across but it might be something completely different, when the consecutive
systems differ reasonably.
However that would suggest that the manner the exchanges are made is
severely wrong in some cases.
Any help to resolve the problem would be greatly appreciated.
XAvier.
On Apr 26, 2013, at 9:21 AM, Mark Abraham mark.j.abra...@gmail.com
wrote:
On Thu, Apr 25, 2013 at 11:05 PM, XAvier Periole x.peri...@rug.nl
wrote:
Thanks for the answer. I'll check gmx4.5.7 and report back.
I am not sure what you mean by GROMACS swaps the coordinates not the
ensemble data. The coupling to P and T and not exchanged with it?
The code in src/kernel/repl_ex.c:
static void exchange_state(const gmx_multisim_t *ms, int b, t_state
*state)
{
/* When t_state changes, this code should be updated. */
int ngtc, nnhpres;
ngtc= state-ngtc * state-nhchainlength;
nnhpres = state-nnhpres* state-nhchainlength;
exchange_rvecs(ms, b, state-box, DIM);
exchange_rvecs(ms, b, state-box_rel, DIM);
exchange_rvecs(ms, b, state-boxv, DIM);
exchange_reals(ms, b, (state-veta), 1);
exchange_reals(ms, b, (state-vol0), 1);
exchange_rvecs(ms, b, state-svir_prev, DIM);
exchange_rvecs(ms, b, state-fvir_prev, DIM);
exchange_rvecs(ms, b, state-pres_prev, DIM);
exchange_doubles(ms, b, state-nosehoover_xi, ngtc);
exchange_doubles(ms, b, state-nosehoover_vxi, ngtc);
exchange_doubles(ms, b, state-nhpres_xi, nnhpres);
exchange_doubles(ms, b
Re: [gmx-users] issue in replica exchange
I saw that redmine report, which could be related but it seems to happen only
for runs done outside the domain and particle decompositions.
I'll fill up a red mine.
Anything I could do to help speeding the fix?
On May 2, 2013, at 11:53 AM, Mark Abraham mark.j.abra...@gmail.com wrote:
On Wed, May 1, 2013 at 10:24 PM, XAvier Periole x.peri...@rug.nl wrote:
Ok here is my current status on that REMD issue.
For info: I use
Temperature: v-rescale, tau_t = 2.0 ps
Pressure: berendsen, tau_p = 5.0 ps,
time step: dt=0.002 - 0.020 fs,
COM removal on for bilayer/water separately
The symptoms: explosion of the system after 2-5 steps following the swap,
first sign is a huge jump in LJ interactions and pressure. This jump seems
to be absorbed by the box size and temperature when possible … see example
I provided earlier. A large VCM (velocity centre of mass?) is often
associated with the crash. But also pressure scaling more than 1% ...
1- the problem mentioned above remains in gmx-4.5.7 and it might actually
got worse. I was able to run a 500 ns simulation with gmx405 using similar
setup as for gmx457. The following point happened in gmx457.
2- it persists with a time step of 2 fs. Actually all tests performed in
the following used dt=2fs.
3- if I perform an exchange that explodes within mdrun myself (externally
to the remd gromacs by getting the gro file with the mdp adjusting the
temperature) it goes all fine.
4- the issue gets much worst when the consecutive replicas differ
(different protein conformations and the box size etc) … explosion at first
exchange.
5- the use of parrinelo-raman does not help
6- cancelling the centre of mass removal does not remove the problem.
7- switching to NVT ensemble does not help but makes it worst (crash in 2
steps). All exchanges accepted at first attempt crash with the message
Large VCM(group SOL): -0.0XXX , -0.XXX, -0.16XXX, Temp-cm:6.55XXX
8- using a unique conformation (the same) for all replicas in the NVT REMD
simulation after equilibration in the same NVT ensemble (for 1 ns) removes
the problem.
9- taking the equilibrated NVT conformations, equilibrate them in an NPT
ensemble (1 ns) and let go the exchanges afterwards restores the problem …
one exchange is not properly done at the second trial, while the first ones
were fine. Well if errors were made that was with reasonable
10- note also that the coarse grain I use is extremely forgiving, meaning
you can perform really nasty transformations and run it further after
simple minimisation … so even abrupt changes in temperatures should be fine
and relax quickly.
11- when looking at the conformations themselves nothing appears to have
jumped over or nothing funky.
At this point I am not sure what to think and what to do next. There is
definitely something not going right during the exchanges.
OK, thanks for the effort. That all agrees with my suspicion that the full
state is not being exchanged.
Anyone has been able to run a REMD simulation in an NPT ensemble without
crashes? I would imagine someone has and something particular to my system
is making it going wrong but I am really wondering what it could be. My
feeling is that something relative to the box size or pressure is not going
across but it might be something completely different, when the consecutive
systems differ reasonably.
I've never tried, but an experiment with a water box might be instructive.
However that would suggest that the manner the exchanges are made is
severely wrong in some cases.
Any help to resolve the problem would be greatly appreciated.
There is an outstanding REMD issue on redmine that could be related (
http://redmine.gromacs.org/issues/1191). I'd suggest you open a new issue
there, upload a minimal set of .tprs that can reproduce the problem and
anything you can think of that might help investigate. For something I'm
doing, I'd like to be sure the full T-coupling state is being exchanged,
and we may as well kill all the bugs at once.
Mark
XAvier.
On Apr 26, 2013, at 9:21 AM, Mark Abraham mark.j.abra...@gmail.com
wrote:
On Thu, Apr 25, 2013 at 11:05 PM, XAvier Periole x.peri...@rug.nl
wrote:
Thanks for the answer. I'll check gmx4.5.7 and report back.
I am not sure what you mean by GROMACS swaps the coordinates not the
ensemble data. The coupling to P and T and not exchanged with it?
The code in src/kernel/repl_ex.c:
static void exchange_state(const gmx_multisim_t *ms, int b, t_state
*state)
{
/* When t_state changes, this code should be updated. */
int ngtc, nnhpres;
ngtc= state-ngtc * state-nhchainlength;
nnhpres = state-nnhpres* state-nhchainlength;
exchange_rvecs(ms, b, state-box, DIM);
exchange_rvecs(ms, b, state-box_rel, DIM);
exchange_rvecs(ms, b, state-boxv, DIM);
exchange_reals(ms, b, (state-veta), 1);
exchange_reals(ms, b, (state-vol0), 1);
exchange_rvecs(ms, b, state
Re: [gmx-users] issue in replica exchange
Could you send me a set of tar files that I could look at things the same way I do with my system? I would guess that 6 tar files where you same energies and print log file every step but xtc and trr files not that often would be really cool. You can send them directly to my email (x.peri...@rug.nl) unless they are too big. If you do not like the idea it is also ok. On May 2, 2013, at 1:38 PM, Simone Conti simone...@gmail.com wrote: Yes, my system is described at atomic level. No, I can't see any strange value around exchanges. I analyzed only a very little number of trajectories, but temperature, volume, potential energy, pressure seem all to be around normal fluctuations. 2013/5/2 XAvier Periole x.peri...@rug.nl Did you look at some data like temperature/pressure/box size/Epot as a function of time and especially around some exchanges? Your system is atomistic I presume. On May 2, 2013, at 12:38 PM, Simone Conti simone...@gmail.com wrote: I'm running remd in NPT ensemble for a small peptide and all is ok if the maximum temperature is below 510/520 kelvin. I use Nosé-Hoover termostat and Parrinello-Rahman barostat. Ref T from 285 to 500K and ref P equals to 1bar. Gromacs version 4.5.5. Exchange trials every 5 ps. If I try to add replica at a higher temperature the system crash, but I think it is a problem of equilibration. 2013/5/1 XAvier Periole x.peri...@rug.nl Ok here is my current status on that REMD issue. For info: I use Temperature: v-rescale, tau_t = 2.0 ps Pressure: berendsen, tau_p = 5.0 ps, time step: dt=0.002 - 0.020 fs, COM removal on for bilayer/water separately The symptoms: explosion of the system after 2-5 steps following the swap, first sign is a huge jump in LJ interactions and pressure. This jump seems to be absorbed by the box size and temperature when possible … see example I provided earlier. A large VCM (velocity centre of mass?) is often associated with the crash. But also pressure scaling more than 1% ... 1- the problem mentioned above remains in gmx-4.5.7 and it might actually got worse. I was able to run a 500 ns simulation with gmx405 using similar setup as for gmx457. The following point happened in gmx457. 2- it persists with a time step of 2 fs. Actually all tests performed in the following used dt=2fs. 3- if I perform an exchange that explodes within mdrun myself (externally to the remd gromacs by getting the gro file with the mdp adjusting the temperature) it goes all fine. 4- the issue gets much worst when the consecutive replicas differ (different protein conformations and the box size etc) … explosion at first exchange. 5- the use of parrinelo-raman does not help 6- cancelling the centre of mass removal does not remove the problem. 7- switching to NVT ensemble does not help but makes it worst (crash in 2 steps). All exchanges accepted at first attempt crash with the message Large VCM(group SOL): -0.0XXX , -0.XXX, -0.16XXX, Temp-cm:6.55XXX 8- using a unique conformation (the same) for all replicas in the NVT REMD simulation after equilibration in the same NVT ensemble (for 1 ns) removes the problem. 9- taking the equilibrated NVT conformations, equilibrate them in an NPT ensemble (1 ns) and let go the exchanges afterwards restores the problem … one exchange is not properly done at the second trial, while the first ones were fine. Well if errors were made that was with reasonable 10- note also that the coarse grain I use is extremely forgiving, meaning you can perform really nasty transformations and run it further after simple minimisation … so even abrupt changes in temperatures should be fine and relax quickly. 11- when looking at the conformations themselves nothing appears to have jumped over or nothing funky. At this point I am not sure what to think and what to do next. There is definitely something not going right during the exchanges. Anyone has been able to run a REMD simulation in an NPT ensemble without crashes? I would imagine someone has and something particular to my system is making it going wrong but I am really wondering what it could be. My feeling is that something relative to the box size or pressure is not going across but it might be something completely different, when the consecutive systems differ reasonably. However that would suggest that the manner the exchanges are made is severely wrong in some cases. Any help to resolve the problem would be greatly appreciated. XAvier. On Apr 26, 2013, at 9:21 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Thu, Apr 25, 2013 at 11:05 PM, XAvier Periole x.peri...@rug.nl wrote: Thanks for the answer. I'll check gmx4.5.7 and report back. I am not sure what you mean by GROMACS swaps the coordinates not the ensemble data. The coupling to P and T and not exchanged with it? The code in src/kernel/repl_ex.c: static void exchange_state(const
Re: [gmx-users] issue in replica exchange
I mean tpr files not tar! Autocorrection is sometimes funny :)) On May 2, 2013, at 2:11 PM, XAvier Periole x.peri...@rug.nl wrote: Could you send me a set of tar files that I could look at things the same way I do with my system? I would guess that 6 tar files where you same energies and print log file every step but xtc and trr files not that often would be really cool. You can send them directly to my email (x.peri...@rug.nl) unless they are too big. If you do not like the idea it is also ok. On May 2, 2013, at 1:38 PM, Simone Conti simone...@gmail.com wrote: Yes, my system is described at atomic level. No, I can't see any strange value around exchanges. I analyzed only a very little number of trajectories, but temperature, volume, potential energy, pressure seem all to be around normal fluctuations. 2013/5/2 XAvier Periole x.peri...@rug.nl Did you look at some data like temperature/pressure/box size/Epot as a function of time and especially around some exchanges? Your system is atomistic I presume. On May 2, 2013, at 12:38 PM, Simone Conti simone...@gmail.com wrote: I'm running remd in NPT ensemble for a small peptide and all is ok if the maximum temperature is below 510/520 kelvin. I use Nosé-Hoover termostat and Parrinello-Rahman barostat. Ref T from 285 to 500K and ref P equals to 1bar. Gromacs version 4.5.5. Exchange trials every 5 ps. If I try to add replica at a higher temperature the system crash, but I think it is a problem of equilibration. 2013/5/1 XAvier Periole x.peri...@rug.nl Ok here is my current status on that REMD issue. For info: I use Temperature: v-rescale, tau_t = 2.0 ps Pressure: berendsen, tau_p = 5.0 ps, time step: dt=0.002 - 0.020 fs, COM removal on for bilayer/water separately The symptoms: explosion of the system after 2-5 steps following the swap, first sign is a huge jump in LJ interactions and pressure. This jump seems to be absorbed by the box size and temperature when possible … see example I provided earlier. A large VCM (velocity centre of mass?) is often associated with the crash. But also pressure scaling more than 1% ... 1- the problem mentioned above remains in gmx-4.5.7 and it might actually got worse. I was able to run a 500 ns simulation with gmx405 using similar setup as for gmx457. The following point happened in gmx457. 2- it persists with a time step of 2 fs. Actually all tests performed in the following used dt=2fs. 3- if I perform an exchange that explodes within mdrun myself (externally to the remd gromacs by getting the gro file with the mdp adjusting the temperature) it goes all fine. 4- the issue gets much worst when the consecutive replicas differ (different protein conformations and the box size etc) … explosion at first exchange. 5- the use of parrinelo-raman does not help 6- cancelling the centre of mass removal does not remove the problem. 7- switching to NVT ensemble does not help but makes it worst (crash in 2 steps). All exchanges accepted at first attempt crash with the message Large VCM(group SOL): -0.0XXX , -0.XXX, -0.16XXX, Temp-cm:6.55XXX 8- using a unique conformation (the same) for all replicas in the NVT REMD simulation after equilibration in the same NVT ensemble (for 1 ns) removes the problem. 9- taking the equilibrated NVT conformations, equilibrate them in an NPT ensemble (1 ns) and let go the exchanges afterwards restores the problem … one exchange is not properly done at the second trial, while the first ones were fine. Well if errors were made that was with reasonable 10- note also that the coarse grain I use is extremely forgiving, meaning you can perform really nasty transformations and run it further after simple minimisation … so even abrupt changes in temperatures should be fine and relax quickly. 11- when looking at the conformations themselves nothing appears to have jumped over or nothing funky. At this point I am not sure what to think and what to do next. There is definitely something not going right during the exchanges. Anyone has been able to run a REMD simulation in an NPT ensemble without crashes? I would imagine someone has and something particular to my system is making it going wrong but I am really wondering what it could be. My feeling is that something relative to the box size or pressure is not going across but it might be something completely different, when the consecutive systems differ reasonably. However that would suggest that the manner the exchanges are made is severely wrong in some cases. Any help to resolve the problem would be greatly appreciated. XAvier. On Apr 26, 2013, at 9:21 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Thu, Apr 25, 2013 at 11:05 PM, XAvier Periole x.peri...@rug.nl wrote: Thanks for the answer. I'll check gmx4.5.7 and report back. I am not sure what you mean by GROMACS swaps the coordinates not the ensemble
Re: [gmx-users] issue in replica exchange
You mean working with or working on the code? I'll try gmx-4.6.1 On May 2, 2013, at 2:26 PM, Michael Shirts mrshi...@gmail.com wrote: Quick check here -- is 4.6 behaving correctly? I actually spent some time working on REMD in 4.6, and it seems to be behaving correctly in my hands with temperature and pressure control. Thanks for any additional info on this! On Thu, May 2, 2013 at 8:18 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Thu, May 2, 2013 at 12:58 PM, XAvier Periole x.peri...@rug.nl wrote: I saw that redmine report, which could be related but it seems to happen only for runs done outside the domain and particle decompositions. I'll fill up a red mine. Anything I could do to help speeding the fix? What'd be really nice is some thought on how one can demonstrate that the implementation of the exchange matches what would be expected from the theory. For T-exchange under NVT, it is sufficient to rescale velocities and quantities derived from them by the correct factor. That includes various things like T-coupling history and integrator half-step quantities (and does REMD with leap-frog make sense anyway?). For NPT, there's probably also some P-coupling quantities to scale, and the box to exchange. Anything I've missed? Hopefully virial contributions don't matter either way? Perhaps a decent first step is to hack the code to do a self exchange, by clearing the entire state and rebuilding with what would/should be received from an exchange with a hypothethetical replica in an identical pre-exchange state. Only if the code can do that (i.e. mdrun -reprod produces a trajectory indistinguishable from a run that does not attempt this self exchange) is it worth considering proper state exchanges, and the process of making the code do the former should illustrate what is required for the latter. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] issue in replica exchange
Some good news … The tpr files provided by Simone do NOT show abnormal behaviour! This good news :)) However after turning ON the particle decomposition option to mdrun (-pd) I got a warnings of water not being able to be settled and a crash. This was still with Simone's trips … I took that as a good sign! Then I went back to my system and changed the topology to be able to turn OFF the particle decomposition that I need to use due to a long bond … the system when right trough 650 ps with many exchanges without a complain. I would have to check the continuity in the energies, Temp and other but it seems to be quite clear: The problem I am facing is located in the particle decomposition section of the code. I will fill a redmine and let see how to proceed from there. I won't be able to do this before middle of next week though. Tks for your help, XAvier. On May 2, 2013, at 2:36 PM, Michael Shirts mrshi...@gmail.com wrote: Both. So if 4.6.1 doesn't work, I want to know so we can patch it before 4.6.2 comes out. If it does work, then there is probably stuff that can be backported. On Thu, May 2, 2013 at 8:32 AM, XAvier Periole x.peri...@rug.nl wrote: You mean working with or working on the code? I'll try gmx-4.6.1 On May 2, 2013, at 2:26 PM, Michael Shirts mrshi...@gmail.com wrote: Quick check here -- is 4.6 behaving correctly? I actually spent some time working on REMD in 4.6, and it seems to be behaving correctly in my hands with temperature and pressure control. Thanks for any additional info on this! On Thu, May 2, 2013 at 8:18 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Thu, May 2, 2013 at 12:58 PM, XAvier Periole x.peri...@rug.nl wrote: I saw that redmine report, which could be related but it seems to happen only for runs done outside the domain and particle decompositions. I'll fill up a red mine. Anything I could do to help speeding the fix? What'd be really nice is some thought on how one can demonstrate that the implementation of the exchange matches what would be expected from the theory. For T-exchange under NVT, it is sufficient to rescale velocities and quantities derived from them by the correct factor. That includes various things like T-coupling history and integrator half-step quantities (and does REMD with leap-frog make sense anyway?). For NPT, there's probably also some P-coupling quantities to scale, and the box to exchange. Anything I've missed? Hopefully virial contributions don't matter either way? Perhaps a decent first step is to hack the code to do a self exchange, by clearing the entire state and rebuilding with what would/should be received from an exchange with a hypothethetical replica in an identical pre-exchange state. Only if the code can do that (i.e. mdrun -reprod produces a trajectory indistinguishable from a run that does not attempt this self exchange) is it worth considering proper state exchanges, and the process of making the code do the former should illustrate what is required for the latter. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users
Re: [gmx-users] issue in replica exchange
I'll look at the 4.6.1 version next week, I could install it but I got a conflict between the environmental variable defining openMP variable but I turned it off during compilation … You could try to run on particle decomposition to see if you get a problem … it should one quite quick. On May 2, 2013, at 2:36 PM, Michael Shirts mrshi...@gmail.com wrote: Both. So if 4.6.1 doesn't work, I want to know so we can patch it before 4.6.2 comes out. If it does work, then there is probably stuff that can be backported. On Thu, May 2, 2013 at 8:32 AM, XAvier Periole x.peri...@rug.nl wrote: You mean working with or working on the code? I'll try gmx-4.6.1 On May 2, 2013, at 2:26 PM, Michael Shirts mrshi...@gmail.com wrote: Quick check here -- is 4.6 behaving correctly? I actually spent some time working on REMD in 4.6, and it seems to be behaving correctly in my hands with temperature and pressure control. Thanks for any additional info on this! On Thu, May 2, 2013 at 8:18 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Thu, May 2, 2013 at 12:58 PM, XAvier Periole x.peri...@rug.nl wrote: I saw that redmine report, which could be related but it seems to happen only for runs done outside the domain and particle decompositions. I'll fill up a red mine. Anything I could do to help speeding the fix? What'd be really nice is some thought on how one can demonstrate that the implementation of the exchange matches what would be expected from the theory. For T-exchange under NVT, it is sufficient to rescale velocities and quantities derived from them by the correct factor. That includes various things like T-coupling history and integrator half-step quantities (and does REMD with leap-frog make sense anyway?). For NPT, there's probably also some P-coupling quantities to scale, and the box to exchange. Anything I've missed? Hopefully virial contributions don't matter either way? Perhaps a decent first step is to hack the code to do a self exchange, by clearing the entire state and rebuilding with what would/should be received from an exchange with a hypothethetical replica in an identical pre-exchange state. Only if the code can do that (i.e. mdrun -reprod produces a trajectory indistinguishable from a run that does not attempt this self exchange) is it worth considering proper state exchanges, and the process of making the code do the former should illustrate what is required for the latter. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] issue in replica exchange
Are confirming that you reproduce the problem with gmx-4.6.1 or simply summarizing in case we lose track :)) On May 2, 2013, at 23:31, Michael Shirts mrshi...@gmail.com wrote: So to summarize -- the problem appears to be with particle decomposition. On Thu, May 2, 2013 at 4:15 PM, XAvier Periole x.peri...@rug.nl wrote: I'll look at the 4.6.1 version next week, I could install it but I got a conflict between the environmental variable defining openMP variable but I turned it off during compilation … You could try to run on particle decomposition to see if you get a problem … it should one quite quick. On May 2, 2013, at 2:36 PM, Michael Shirts mrshi...@gmail.com wrote: Both. So if 4.6.1 doesn't work, I want to know so we can patch it before 4.6.2 comes out. If it does work, then there is probably stuff that can be backported. On Thu, May 2, 2013 at 8:32 AM, XAvier Periole x.peri...@rug.nl wrote: You mean working with or working on the code? I'll try gmx-4.6.1 On May 2, 2013, at 2:26 PM, Michael Shirts mrshi...@gmail.com wrote: Quick check here -- is 4.6 behaving correctly? I actually spent some time working on REMD in 4.6, and it seems to be behaving correctly in my hands with temperature and pressure control. Thanks for any additional info on this! On Thu, May 2, 2013 at 8:18 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Thu, May 2, 2013 at 12:58 PM, XAvier Periole x.peri...@rug.nl wrote: I saw that redmine report, which could be related but it seems to happen only for runs done outside the domain and particle decompositions. I'll fill up a red mine. Anything I could do to help speeding the fix? What'd be really nice is some thought on how one can demonstrate that the implementation of the exchange matches what would be expected from the theory. For T-exchange under NVT, it is sufficient to rescale velocities and quantities derived from them by the correct factor. That includes various things like T-coupling history and integrator half-step quantities (and does REMD with leap-frog make sense anyway?). For NPT, there's probably also some P-coupling quantities to scale, and the box to exchange. Anything I've missed? Hopefully virial contributions don't matter either way? Perhaps a decent first step is to hack the code to do a self exchange, by clearing the entire state and rebuilding with what would/should be received from an exchange with a hypothethetical replica in an identical pre-exchange state. Only if the code can do that (i.e. mdrun -reprod produces a trajectory indistinguishable from a run that does not attempt this self exchange) is it worth considering proper state exchanges, and the process of making the code do the former should illustrate what is required for the latter. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http
Re: [gmx-users] local pressure
The use of the original code is quite straightforward, the post processing is a bit more confusing but quite accessible. We have been using this code (the one available on the site) and related version in the lab and we definitely would find it very sad to not keep this feature available in GROMACS. On May 1, 2013, at 2:34 AM, Justin Lemkul jalem...@vt.edu wrote: On 4/30/13 8:01 PM, Sikandar Mashayak wrote: Hi I found the branch of gromacs code called localpressure-4.0 at http://redmine.gromacs.org/projects/gromacs/repository/show?rev=localpressure-4-0. I am wondering whether this code can compute the spatial variation of pressure in given system. And if it does, how stable is this branch? Are there any known issues with it? And any particular reason this is not included in main gromacs releases? Lack of documentation has made it very difficult to use, it is extremely slow, and no one ever asks about it except once every few years. All of those factors make it unlikely to ever incorporate into an actual release. Given that the development process has gone on for years in the absence of any real interest in the localpressure branch, it's probably more trouble than it's worth to get it up and running effectively. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] local pressure
Well I am not the expert. O.H.S. Ollila, M. Louhivuori and E. Lindahl are :)). The paper related to the use would be: Ollila et al, PRL 102, 078101 (2009) Ollila et al, Biophysical Journal (100)1651–59 On May 1, 2013, at 5:48 PM, Sikandar Mashayak symasha...@gmail.com wrote: Thanks Xavier Can you please elaborate on how to use and post-process the local pressure version of gromacs? Do you have any examples or reference article? May be you can create a HowTo wiki as Justin suggested, it would be of great help. Thanks Sikandar On Wed, May 1, 2013 at 5:03 AM, Justin Lemkul jalem...@vt.edu wrote: On 5/1/13 5:12 AM, XAvier Periole wrote: The use of the original code is quite straightforward, the post processing is a bit more confusing but quite accessible. That would be a great topic for a wiki How-To. We have been using this code (the one available on the site) and related version in the lab and we definitely would find it very sad to not keep this feature available in GROMACS. I never said it would go away, but given the fact that there have been no updates to the git branch in over 3 years, it's simply unlikely that anyone has cared to move it forward. If someone wants to update the code to be compatible with 4.6, that would be a welcome contribution. Lack of any request for improvements and inclusion in an official release has likely led to the decline in interest from the development team. If you want something included, you should file a feature request on redmine.gromacs.org - it's the only official way we keep track of fixes and features. If it's not there, it likely won't get addressed until one of the developers has a compelling need to work on it. -Justin On May 1, 2013, at 2:34 AM, Justin Lemkul jalem...@vt.edu wrote: On 4/30/13 8:01 PM, Sikandar Mashayak wrote: Hi I found the branch of gromacs code called localpressure-4.0 at http://redmine.gromacs.org/**projects/gromacs/repository/** show?rev=localpressure-4-0http://redmine.gromacs.org/projects/gromacs/repository/show?rev=localpressure-4-0 . I am wondering whether this code can compute the spatial variation of pressure in given system. And if it does, how stable is this branch? Are there any known issues with it? And any particular reason this is not included in main gromacs releases? Lack of documentation has made it very difficult to use, it is extremely slow, and no one ever asks about it except once every few years. All of those factors make it unlikely to ever incorporate into an actual release. Given that the development process has gone on for years in the absence of any real interest in the localpressure branch, it's probably more trouble than it's worth to get it up and running effectively. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post
Re: [gmx-users] issue in replica exchange
Ok here is my current status on that REMD issue.
For info: I use
Temperature: v-rescale, tau_t = 2.0 ps
Pressure: berendsen, tau_p = 5.0 ps,
time step: dt=0.002 - 0.020 fs,
COM removal on for bilayer/water separately
The symptoms: explosion of the system after 2-5 steps following the swap, first
sign is a huge jump in LJ interactions and pressure. This jump seems to be
absorbed by the box size and temperature when possible … see example I provided
earlier. A large VCM (velocity centre of mass?) is often associated with the
crash. But also pressure scaling more than 1% ...
1- the problem mentioned above remains in gmx-4.5.7 and it might actually got
worse. I was able to run a 500 ns simulation with gmx405 using similar setup as
for gmx457. The following point happened in gmx457.
2- it persists with a time step of 2 fs. Actually all tests performed in the
following used dt=2fs.
3- if I perform an exchange that explodes within mdrun myself (externally to
the remd gromacs by getting the gro file with the mdp adjusting the
temperature) it goes all fine.
4- the issue gets much worst when the consecutive replicas differ (different
protein conformations and the box size etc) … explosion at first exchange.
5- the use of parrinelo-raman does not help
6- cancelling the centre of mass removal does not remove the problem.
7- switching to NVT ensemble does not help but makes it worst (crash in 2
steps). All exchanges accepted at first attempt crash with the message Large
VCM(group SOL): -0.0XXX , -0.XXX, -0.16XXX, Temp-cm:6.55XXX
8- using a unique conformation (the same) for all replicas in the NVT REMD
simulation after equilibration in the same NVT ensemble (for 1 ns) removes the
problem.
9- taking the equilibrated NVT conformations, equilibrate them in an NPT
ensemble (1 ns) and let go the exchanges afterwards restores the problem … one
exchange is not properly done at the second trial, while the first ones were
fine. Well if errors were made that was with reasonable
10- note also that the coarse grain I use is extremely forgiving, meaning you
can perform really nasty transformations and run it further after simple
minimisation … so even abrupt changes in temperatures should be fine and relax
quickly.
11- when looking at the conformations themselves nothing appears to have jumped
over or nothing funky.
At this point I am not sure what to think and what to do next. There is
definitely something not going right during the exchanges.
Anyone has been able to run a REMD simulation in an NPT ensemble without
crashes? I would imagine someone has and something particular to my system is
making it going wrong but I am really wondering what it could be. My feeling is
that something relative to the box size or pressure is not going across but it
might be something completely different, when the consecutive systems differ
reasonably.
However that would suggest that the manner the exchanges are made is severely
wrong in some cases.
Any help to resolve the problem would be greatly appreciated.
XAvier.
On Apr 26, 2013, at 9:21 AM, Mark Abraham mark.j.abra...@gmail.com wrote:
On Thu, Apr 25, 2013 at 11:05 PM, XAvier Periole x.peri...@rug.nl wrote:
Thanks for the answer. I'll check gmx4.5.7 and report back.
I am not sure what you mean by GROMACS swaps the coordinates not the
ensemble data. The coupling to P and T and not exchanged with it?
The code in src/kernel/repl_ex.c:
static void exchange_state(const gmx_multisim_t *ms, int b, t_state *state)
{
/* When t_state changes, this code should be updated. */
int ngtc, nnhpres;
ngtc= state-ngtc * state-nhchainlength;
nnhpres = state-nnhpres* state-nhchainlength;
exchange_rvecs(ms, b, state-box, DIM);
exchange_rvecs(ms, b, state-box_rel, DIM);
exchange_rvecs(ms, b, state-boxv, DIM);
exchange_reals(ms, b, (state-veta), 1);
exchange_reals(ms, b, (state-vol0), 1);
exchange_rvecs(ms, b, state-svir_prev, DIM);
exchange_rvecs(ms, b, state-fvir_prev, DIM);
exchange_rvecs(ms, b, state-pres_prev, DIM);
exchange_doubles(ms, b, state-nosehoover_xi, ngtc);
exchange_doubles(ms, b, state-nosehoover_vxi, ngtc);
exchange_doubles(ms, b, state-nhpres_xi, nnhpres);
exchange_doubles(ms, b, state-nhpres_vxi, nnhpres);
exchange_doubles(ms, b, state-therm_integral, state-ngtc);
exchange_rvecs(ms, b, state-x, state-natoms);
exchange_rvecs(ms, b, state-v, state-natoms);
exchange_rvecs(ms, b, state-sd_X, state-natoms);
}
I mis-stated last night - there *is* exchange of ensemble data, but it is
incomplete. In particular, state-ekinstate is not exchanged. Probably it
is incomplete because the 9-year-old comment about t_state changing is in a
location that nobody changing t_state will see. And serializing a complex C
data structure over MPI is tedious at best. But that is not really an
excuse for the non-modularity GROMACS has for many of its key data
Re: [gmx-users] Re: genbox box size problem
We have noticed that g_genbox issue with MARTINI but have not new able to understand where it actually comes from. It might be a bug or just a miss communication of the vdw radius with genbox that appears only with large spheres. On Apr 29, 2013, at 19:50, alex.bjorling alex.bjorl...@gmail.com wrote: Justin Lemkul wrote I have seen this exact problem posted before. The coordinates of the water box provided by MARTINI have some coordinate values that basically coincide across the periodic box. With genconf, you can apply the -dist option to space them out slightly, then re-equilibrate before using the new configuration as input into genbox. I don't think that's true. Stacking boxes with -nbox 3 3 3 (without -dist) gives a big box which you can minimize and equilibrate with no trouble. Both with and without -dist 0.21 0.21 0.21 (0.21 is a suitable MARTINI -vdwd for genbox), you get big water boxes which behave well. The problems start when you use them as solvents in genbox. Xavier's suggestion (stack, minimize, equilibrate, manually cut with a script) works fine, thanks for the suggestion. Seems to me there might be a bug in genbox, but I'm not the right person to make such claims. Alex -- View this message in context: http://gromacs.5086.x6.nabble.com/genbox-box-size-problem-tp5007753p5007768.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] genbox box size problem
genbox works best when the box size of the solute is defined as the same as of the water one used to solvate it. So you can build a water box with the dimensions you want and them use it. You can build a water box by using genconf -nbox and use a script to cut to the dimensions you need, minimize, equilibrate ... Using a bigger box size should work too but it might need to be positioned/centered correctly and the solute too ... On Apr 29, 2013, at 11:30, Alexander Björling alex.bjorl...@gmail.com wrote: Dear users, I am trying to solvate a MARTINI model, using a pre-equilibrated coarse-grained water box. This usually works fine with the following command. genbox -cs water-1bar-303K.gro -cp 01min.gro -o 02solv -vdwd 0.21 When I recently increased the box size things started going wrong. As the simulation box got bigger than the (-cs) water box, the solvated structure ended up containing clear block-shaped regions of higher and lower solvent density. I obviously tried stacking the (-cs) box first to make it bigger than the box in the (-cp) file, genconf -f water-1bar-303K.gro -o water-1bar-303K_big.gro -nbox 3 3 3 but the problem persisted. Waters actually coincide in the solvated structure, so energy minimization is obviously hopeless. Is genbox behaving unexpectedly or is this likely an input problem? Cheers, Alex -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Questions about the MFFA boundery implementation of Gromacs?
It is not clear what you are asking. Could you try to reformulate your problem/question? Did you read the Louhivuori-PNAS papers? There are lots of details in the supplementary material. On Apr 27, 2013, at 6:43, song.yongshun song.yongs...@163.com wrote: Dear all: I was using the MFFA version of Gromacs which is provided by m.j.louhivuori at http://md.chem.rug.nl/~mara/mffa.html. I have some quesition about this version: i.I saw the implementation of MFFA always with the flip-flop of lipid.Can I apply the flip-flop with this MFFA version of Gromacs ? ii.I also saw the description of implementation of MFFA along only one direction.Is this available in this MFFA version of Gromacs? Anyone who is familar with it help me. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] RE: Martini with PME, temp two low
nstlist of 2 is a be extreme! Did you try 5! It should be fine … but if your are happy that's ok :)) On Apr 26, 2013, at 12:37 PM, ABEL Stephane 175950 stephane.a...@cea.fr wrote: Hi Xavier, I used a dt of 10 ps with nstlist of 2. In that case the Temp of the system is stable and the energy well conserved (400 ns of run). I do know if it is optimal but it works for my system. Stephane -- Message: 1 Date: Fri, 26 Apr 2013 07:58:12 +0200 From: XAvier Periole x.peri...@rug.nl Subject: Re: [gmx-users] Re: Martini with PME, temp two low (ABEL Stephane 175950) To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 6d1fd74e-91bb-4c0c-95ce-e863924dd...@rug.nl Content-Type: text/plain; charset=us-ascii Good. Note however that we do get the right temperature with a dt=20fs with Martini so you energy leak might be in the cutoff scheme or the system is really badly equilibrated. On Apr 25, 2013, at 18:23, ABEL Stephane 175950 stephane.a...@cea.fr wrote: Xavier I have followed your suggestion and did a longer NPT equilibration with smaller dt and ntlist values and It works. The Energy and Temp reach to stables values as i want. thank you again for your help Stephane -- Message: 2 Date: Thu, 25 Apr 2013 14:17:00 + From: ABEL Stephane 175950 stephane.a...@cea.fr Subject: [gmx-users] Re: Martini with PME, temp two low To: gmx-users@gromacs.org gmx-users@gromacs.org Message-ID: 3e39b768bb199548ab18f7289e7534af1a818...@exdag0-b0.intra.cea.fr Content-Type: text/plain; charset=us-ascii @ Vitaly of course. I know that. My system is neutral but with charged particles (AOT and Na+). @Xavier I will try your suggestion and equilibrate my system for a longer period Thanks again Stephane -- Message: 1 Date: Thu, 25 Apr 2013 15:52:09 +0200 From: XAvier Periole x.peri...@rug.nl Subject: Re: [gmx-users] Martini with PME, temp two low To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 0a7b7d0a-b419-4d3d-826b-e6d61de6d...@rug.nl Content-Type: text/plain; charset=windows-1252 Well ? 400 ps is rather small and you can expect deviations from so short simulations if you start from an non-equilibrated system. I am not sure what the void is but this indicates that your system might not be equilibrated ? You can try to decrease the time step and nstlist to see if you the drop of temperature is due a flow of energy. On Apr 25, 2013, at 3:26 PM, ABEL Stephane 175950 stephane.a...@cea.fr wrote: Hello Xavier, Thank you for your response. nstlist = 10 and the rlist = 1.0 My mistake, i did not changes these values when i switched to PME, I have rerun the simulations for 400 ps in NPT with these changes and plotted Epot and Temp vs Time The Epot and Temp values are not stables. The average Temp of the system is better than previously but fluctuate around (294 K) instead of 298 K . Note i use gmx4.5.5 to do my calculations. I have also visualized my system at the end of the NPT run, the na+, water, surfactant, octane molecules form a slab with void What's wrong ? Stephane -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] issue in replica exchange
Hi, I have been recently using the REMD code in gmx-407 and gmx-453 and got a few systems crashing for unclear reasons so far. The main tests I made are using gmx407 but it is all reproducible with gmx453. The crashing was also reproduced (not necessarily at the same time point) on several architectures. The system is made of a pair of proteins in a membrane patch and for which the relative orientation is controlled by non-native bond/angles/dihedrals to perform an umbrella sampling. I use the MARTINI force field but that might not be relevant here. The crashes occur following exchanges that do not seem to occur the correct way and preceded by pressure scaling warnings … indicative of a strong destabilisation of the system and eventual explosion. Some information seems to be exchanged inaccurately. Trying to nail down the problem I got stuck and may be some one can help. I placed a pdf file showing plots of bonded/nonbonded energies, temperatures, box size etc … around an exchange that does not lead to a crash (here: md.chem.rug.nl/~periole/remd-issue.pdf). I plotted stuff every step with the temperature colour coded as indicated in the first figure. From the figure it appears that the step right after the exchange there is a huge jump of Potential energy coming from the LJ(SR) part of it. Although there are some small discontinuities in the progression of the bond and angle energy around the exchange they seem to fine. The temperature and box size seem to respond to it a few step latter while the pressure seems to be affected right away but potentially as the Epot will affect the viral and thus the Pressure. The other potential clue is that the jumps reduce with the strength of the pressure coupling. A 1/2 ps tau_p (Berendsen) will lead to a crash while a 5/10/20 ps won't. Inspection of the time evolution of the Epot, box … indicates that the magnitude of the jumps is reduced and the system ca handle the problem. One additional info since I first posted the problem (delayed by the file first attached but now given with a link) the problem is accentuated when the replicas differ in conformation. I am looking at the actual differences as you'll read this email. That is as far as I could go. Any suggestion is welcome. XAvier. MD-Group / Univ. of Groningen The Netherlands-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Martini with PME, temp two low
Did you visualise the system? T in function of time? Epot in function of time? As a side note (not relevant for PME) the mix of nstlist = 10 and the rlist = 1.0 is pretty bad! You want at least rlist=1.2 when nstlist=5 and rlist=1.4 if nstlist =10. On Apr 25, 2013, at 1:10 PM, ABEL Stephane 175950 stephane.a...@cea.fr wrote: Hello all, I am trying to test the martini force field with PME for a charged system that contains na+, water, surfactant, octane molecules at 298K and P=0.1MPa. My system works well, if i use the standard shift parameters (correct temp, and pressure). But for for the simulation with PME , the temp of the system decrease to 290 K. Below my *.mdp parameters for a NPT equil at 298K integrator = md dt = 0.020 nsteps = 1 ; 200ps nstcomm = 10 comm-grps= ;refcoord_scaling = com nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 1000 nstenergy= 100 ;nstxtcout= 1000 xtc_precision= 100 ;xtc-grps = energygrps = AOT W ION OCT nstlist = 10 ns_type = grid pbc = xyz rlist= 1. ; PME parameters coulombtype = PME rcoulomb = 1.2 rvdw = 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 4 tcoupl = v-rescale tc-grps = AOT_W_ION OCT tau_t= 1.0 1.0 ref_t= 298 298 Pcoupl = berendsen Pcoupltype = isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 ;gen_vel = no ;gen_temp = 0 ;gen_seed = 473529 ; MARTINI and CONSTRAINTS ; for ring systems and stiff bonds constraints are defined ; which are best handled using Lincs. constraints = none constraint_algorithm = Lincs unconstrained_start = no lincs_order = 4 lincs_warnangle = 3 Results obtained with W/ PME Statistics over 10001 steps using 1001 frames Energies (kJ/mol) Bond G96AngleLJ (SR) Coulomb (SR) Coul. recip. 1.63789e+041.25195e+03 -4.02093e+05 -8.22079e+03 -4.86843e+04 PotentialKinetic En. Total EnergyTemperature Pressure (bar) -4.41367e+057.81801e+04 -3.63187e+052.90373e+02 -1.76470e+01 T-AOT_W_ION T-OCT 2.90629e+022.90357e+02 Results W:o PME Energies (kJ/mol) Bond G96AngleLJ (SR) Coulomb (SR) Potential 1.60482e+041.24820e+03 -3.34608e+05 -7.33665e+02 -3.18046e+05 Kinetic En. Total EnergyTemperature Pressure (bar) 8.02685e+04 -2.3e+052.98129e+02 -3.07123e+01 Box-X Box-Y Box-Z 1.52926e+011.52926e+011.52926e+01 T-AOT_W_ION T-OCT 2.98141e+022.98129e+02 Did I miss something ? Note that for the moment i do not use the polarizable water model. Thanks for your help Stephane -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Martini with PME, temp two low
Well … 400 ps is rather small and you can expect deviations from so short simulations if you start from an non-equilibrated system. I am not sure what the void is but this indicates that your system might not be equilibrated … You can try to decrease the time step and nstlist to see if you the drop of temperature is due a flow of energy. On Apr 25, 2013, at 3:26 PM, ABEL Stephane 175950 stephane.a...@cea.fr wrote: Hello Xavier, Thank you for your response. nstlist = 10 and the rlist = 1.0 My mistake, i did not changes these values when i switched to PME, I have rerun the simulations for 400 ps in NPT with these changes and plotted Epot and Temp vs Time The Epot and Temp values are not stables. The average Temp of the system is better than previously but fluctuate around (294 K) instead of 298 K . Note i use gmx4.5.5 to do my calculations. I have also visualized my system at the end of the NPT run, the na+, water, surfactant, octane molecules form a slab with void What's wrong ? Stephane -- Message: 5 Date: Thu, 25 Apr 2013 13:34:21 +0200 From: XAvier Periole x.peri...@rug.nl Subject: Re: [gmx-users] Martini with PME, temp two low To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4632c83b-cd6f-4c92-b887-a1c39dff4...@rug.nl Content-Type: text/plain; charset=us-ascii Did you visualise the system? T in function of time? Epot in function of time? As a side note (not relevant for PME) the mix of nstlist = 10 and the rlist = 1.0 is pretty bad! You want at least rlist=1.2 when nstlist=5 and rlist=1.4 if nstlist =10. On Apr 25, 2013, at 1:10 PM, ABEL Stephane 175950 stephane.a...@cea.fr wrote: Hello all, I am trying to test the martini force field with PME for a charged system that contains na+, water, surfactant, octane molecules at 298K and P=0.1MPa. My system works well, if i use the standard shift parameters (correct temp, and pressure). But for for the simulation with PME , the temp of the system decrease to 290 K. Below my *.mdp parameters for a NPT equil at 298K integrator = md dt = 0.020 nsteps = 1 ; 200ps nstcomm = 10 comm-grps= ;refcoord_scaling = com nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 1000 nstenergy= 100 ;nstxtcout= 1000 xtc_precision= 100 ;xtc-grps = energygrps = AOT W ION OCT nstlist = 10 ns_type = grid pbc = xyz rlist= 1. ; PME parameters coulombtype = PME rcoulomb = 1.2 rvdw = 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 4 tcoupl = v-rescale tc-grps = AOT_W_ION OCT tau_t= 1.0 1.0 ref_t= 298 298 Pcoupl = berendsen Pcoupltype = isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 ;gen_vel = no ;gen_temp = 0 ;gen_seed = 473529 ; MARTINI and CONSTRAINTS ; for ring systems and stiff bonds constraints are defined ; which are best handled using Lincs. constraints = none constraint_algorithm = Lincs unconstrained_start = no lincs_order = 4 lincs_warnangle = 3 Results obtained with W/ PME Statistics over 10001 steps using 1001 frames Energies (kJ/mol) Bond G96AngleLJ (SR) Coulomb (SR) Coul. recip. 1.63789e+041.25195e+03 -4.02093e+05 -8.22079e+03 -4.86843e+04 PotentialKinetic En. Total EnergyTemperature Pressure (bar) -4.41367e+057.81801e+04 -3.63187e+052.90373e+02 -1.76470e+01 T-AOT_W_ION T-OCT 2.90629e+022.90357e+02 Results W:o PME Energies (kJ/mol) Bond G96AngleLJ (SR) Coulomb (SR) Potential 1.60482e+041.24820e+03 -3.34608e+05 -7.33665e+02 -3.18046e+05 Kinetic En. Total EnergyTemperature Pressure (bar) 8.02685e+04 -2.3e+052.98129e+02 -3.07123e+01 Box-X Box-Y Box-Z 1.52926e+011.52926e+011.52926e+01 T-AOT_W_ION T-OCT 2.98141e+022.98129e+02 Did I miss something ? Note that for the moment i do not use the polarizable water model. Thanks for your help Stephane -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support
Re: [gmx-users] issue in replica exchange
Thanks for the answer. I'll check gmx4.5.7 and report back. I am not sure what you mean by GROMACS swaps the coordinates not the ensemble data. The coupling to P and T and not exchanged with it? That would explain what I see, but let see what 4.5.7 has to say first. Tks. On Apr 25, 2013, at 22:40, Mark Abraham mark.j.abra...@gmail.com wrote: Thanks for the good report. There have been some known issues about the timing of coupling stages with respect to various intervals between GROMACS events for some algorithms. There are a lot of fixed problems in 4.5.7 that are not specific to REMD, but I have a few lingering doubts about whether we should be exchanging (scaled) coupling values along with the coordinates. (Unlike most REMD implementations, GROMACS swaps the coordinates, not the ensemble data.) If you can reproduce those kinds of symptoms in 4.5.7 (whether or not they then crash) then there looks like there may be a problem with the REMD implementation that is perhaps evident only with the kind of large time step Martini takes? Mark On Thu, Apr 25, 2013 at 1:28 PM, XAvier Periole x.peri...@rug.nl wrote: Hi, I have been recently using the REMD code in gmx-407 and gmx-453 and got a few systems crashing for unclear reasons so far. The main tests I made are using gmx407 but it is all reproducible with gmx453. The crashing was also reproduced (not necessarily at the same time point) on several architectures. The system is made of a pair of proteins in a membrane patch and for which the relative orientation is controlled by non-native bond/angles/dihedrals to perform an umbrella sampling. I use the MARTINI force field but that might not be relevant here. The crashes occur following exchanges that do not seem to occur the correct way and preceded by pressure scaling warnings … indicative of a strong destabilisation of the system and eventual explosion. Some information seems to be exchanged inaccurately. Trying to nail down the problem I got stuck and may be some one can help. I placed a pdf file showing plots of bonded/nonbonded energies, temperatures, box size etc … around an exchange that does not lead to a crash (here: md.chem.rug.nl/~periole/remd-issue.pdf). I plotted stuff every step with the temperature colour coded as indicated in the first figure. From the figure it appears that the step right after the exchange there is a huge jump of Potential energy coming from the LJ(SR) part of it. Although there are some small discontinuities in the progression of the bond and angle energy around the exchange they seem to fine. The temperature and box size seem to respond to it a few step latter while the pressure seems to be affected right away but potentially as the Epot will affect the viral and thus the Pressure. The other potential clue is that the jumps reduce with the strength of the pressure coupling. A 1/2 ps tau_p (Berendsen) will lead to a crash while a 5/10/20 ps won't. Inspection of the time evolution of the Epot, box … indicates that the magnitude of the jumps is reduced and the system ca handle the problem. One additional info since I first posted the problem (delayed by the file first attached but now given with a link) the problem is accentuated when the replicas differ in conformation. I am looking at the actual differences as you'll read this email. That is as far as I could go. Any suggestion is welcome. XAvier. MD-Group / Univ. of Groningen The Netherlands-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Martini with PME, temp two low (ABEL Stephane 175950)
Good. Note however that we do get the right temperature with a dt=20fs with Martini so you energy leak might be in the cutoff scheme or the system is really badly equilibrated. On Apr 25, 2013, at 18:23, ABEL Stephane 175950 stephane.a...@cea.fr wrote: Xavier I have followed your suggestion and did a longer NPT equilibration with smaller dt and ntlist values and It works. The Energy and Temp reach to stables values as i want. thank you again for your help Stephane -- Message: 2 Date: Thu, 25 Apr 2013 14:17:00 + From: ABEL Stephane 175950 stephane.a...@cea.fr Subject: [gmx-users] Re: Martini with PME, temp two low To: gmx-users@gromacs.org gmx-users@gromacs.org Message-ID: 3e39b768bb199548ab18f7289e7534af1a818...@exdag0-b0.intra.cea.fr Content-Type: text/plain; charset=us-ascii @ Vitaly of course. I know that. My system is neutral but with charged particles (AOT and Na+). @Xavier I will try your suggestion and equilibrate my system for a longer period Thanks again Stephane -- Message: 1 Date: Thu, 25 Apr 2013 15:52:09 +0200 From: XAvier Periole x.peri...@rug.nl Subject: Re: [gmx-users] Martini with PME, temp two low To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 0a7b7d0a-b419-4d3d-826b-e6d61de6d...@rug.nl Content-Type: text/plain; charset=windows-1252 Well ? 400 ps is rather small and you can expect deviations from so short simulations if you start from an non-equilibrated system. I am not sure what the void is but this indicates that your system might not be equilibrated ? You can try to decrease the time step and nstlist to see if you the drop of temperature is due a flow of energy. On Apr 25, 2013, at 3:26 PM, ABEL Stephane 175950 stephane.a...@cea.fr wrote: Hello Xavier, Thank you for your response. nstlist = 10 and the rlist = 1.0 My mistake, i did not changes these values when i switched to PME, I have rerun the simulations for 400 ps in NPT with these changes and plotted Epot and Temp vs Time The Epot and Temp values are not stables. The average Temp of the system is better than previously but fluctuate around (294 K) instead of 298 K . Note i use gmx4.5.5 to do my calculations. I have also visualized my system at the end of the NPT run, the na+, water, surfactant, octane molecules form a slab with void What's wrong ? Stephane -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Linear CG beads, grompp doesn't work
I think your original problem is that you define only one charge group for the entire molecule/polymer. You need to define each bead in a separate charge group and things will be fine :)) you do not have charges anyways. As far as I know angles have never made martini unstable but the conventional dihedral potential are not suited for martini or any flexible molecule. XAvier. On Jan 2, 2013, at 4:55, Justin Lemkul jalem...@vt.edu wrote: On 1/1/13 10:51 PM, Xu Dong Huang wrote: @Justin, Does the philosophy described in your tutorial apply to CG martini bead models where 1 bead describes the entire CO2 atom? (If I were to do that, assuming) Presumably. As long as you satisfy the criteria mentioned in the tutorial (moment of inertia and total mass), you should be able to get it to work. I've never dealt with polymers and have very little personal experience with CG models, so I don't know if there are other methodological issues that one might encounter. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error with MARTINI depending by the box size
I have not followed the thread but concerning the solvation of a protein using genbox you need to: 1- use a box of water that has the exact size of the final box you want (you make it yourself using any tool you want) and you need to define the box size of the protein file as the one of the water box conformation. This is given on the last line of the gro file. Then genbox -cp -cs should work fine. 2- you need to use a water box size larger than the one you need. This solution is generally easier. You can generate a box using genconf - nbox option. And again define the box size in the protein conformation file and genbox will just do fine. We generally use -vdwd 0.18. It is a good compromise for disturbing the system the least. Note that these uses have been discussed on the MARTINI forum several times. XAvier. On Dec 11, 2012, at 9:05 AM, francesco oteri wrote: Tanks to all for your advices, I am going to check all the different aspect you suggested and I will report the results as soon as possible. Francesco 2012/12/11 Tsjerk Wassenaar tsje...@gmail.com Hi, Visualization is the key. If you check the structure right after genbox, you should be able to notice something odd. Apparently genbox has a problem with martini water, which probably means there is a problem with monoatomic solvents. The problem has been noted before, b ut I'm a bit too lazy now to check whether it was here or on the martini forum. Using a small box with a single water molecule for filling will solve the problem. Cheers, Tsjerk On Tue, Dec 11, 2012 at 12:06 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Mon, Dec 10, 2012 at 11:54 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/10/12 5:45 PM, francesco oteri wrote: For Justin, I need this water for one simple reason: less then 20nm doesn't workAs I said before It seems you have identified the source of the problem, and it is independent of box size. I questioned the box size because it seemed rather random and you had not shown any data for box sizes less than 19 nm, so I was curious how you arrived at the need for 20 nm, more than double the size of your solute. It would be interesting to see if you could identify a minimum box size that does not require large numbers of solvent configurations to be stacked within the unit cell. The only reason I could see for what you're reporting is if neighboring solvent blocks somehow get crossed to produce overlap when they should simply be next to one another. The larger the box, the greater the probability that this happens. Yeah, that's probably it. The water box has many waters with x coordinates down at 0.000 and near 10.901, with an x size of 10.902. So different box sizes will randomly introduce unstable water configurations according to whether stuff is too close. This water box is probably not suited to the purpose - its box size might not include the half VDW radii outside the water coordinates needed to pack stably. Mark 2012/12/10 francesco oteri francesco.ot...@gmail.com Hi Mark, you are right respect the -vdwd 0.4: In MARTINI tutorials they suggest to use 0.21. Since I still got errors with this procedure, I decided to remove water manually through vmd. Looking carefully at the configurations, I found that the water molecule originating the error is exactly superimposed to an other molecule so I simply deleted it and the same error is reported for an other water molecule. Although I could scan all the pdb to detect all the superimposed water molecules, I believed genbox checked for this. Of course the original box does't contain superimposed molecules. It is highly unusual for genbox to produce overlapping waters, but per the help description, only solute-solvent overlaps are checked, not solvent-solvent, which would likely require enormous amounts of memory (and genbox already has memory issues). -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org
Re: [gmx-users] REMD simulation
Well either you use more replicas or you reduce the temperature range ... There is no way around! On Nov 19, 2012, at 5:54 PM, Kenny Bravo Rodriguez wrote: Dear All, i am trying to performed REMD simulations using Gromacs. My question is concerning the temperature distribution and the number of replica. I need to run 24 replicas of my system with a temperature range of 290-400 K. How can I select the temperatures values for each replica? I tried the server http://folding.bmc.uu.se/remd/index.php but for my system it gives 50 replicas. If i try to take 24 evenly spaced values from the obtained list of temperature then the replicas do not exchange at all. I am using Gromacs 4.5.5 and my system has 6862 water molecules and 535 atoms for the solute. Thanks in advanced Kenny -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulation of charged systems (2)
From what I remember from my earlier impressions ... the equations are not correct when the system is not neutral. In your case the charge is significantly high ... On Nov 2, 2012, at 9:36 AM, Felipe Pineda, PhD wrote: Hi, I recently sent a query, but it was probably not appealing enough to get some feedback. So I try again with a shorter one: Is there any theoretical or technical objection against running an NPgammaT simulation on a charged (total charge = -36) membrane model (hydrated bipolar monolayer) using PME? Many tanks in advance for your input. Best, Felipe +---+ | Luis Felipe Pineda De Castro, PhD | | Computational Chemist - Postdoc | | Linnaeus University | | SE-391 82 Kalmar | | Sweden - Sverige | +---+ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Martini FF for Sec structure changes...
Martini FF cannot model changes in secondary structure ... other CG FF can. You'll find them easily in the literature. Notably the ones from Deserno or Derreumaux. On Oct 10, 2012, at 2:03 PM, rama david wrote: Hi friends, I planed to use the martini force-field for my simulation study of peptide. The peptides are initially alpha-helix in nature. As they come together they formed amyloid fibre( Antiparallel Beta structure). Is it is possible to study the secondary structure backbone study by martini force field. I read in there tutorial that the Secondary structure is predefined therefore they are statics through out the simulation. Conformational changes that produces changes in Sec structure are out of scope in martini. only tertiary structure are free defined to change.. So what to do ??? How to use Martini FF to study secondary structure ??? Is there any way to use coarse grained FF to use for study in Sec. structure??? With Best wishes and regards, Rama David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Martini FF for Sec structure changes...
Nope, but on other softwares. On Oct 10, 2012, at 2:50 PM, rama david wrote: Thank you for your reply, Are these Cg can be used in Gromacs. Thank you in advance. With best wishes and regards, Rama david On Wed, Oct 10, 2012 at 6:13 PM, XAvier Periole x.peri...@rug.nl wrote: Martini FF cannot model changes in secondary structure ... other CG FF can. You'll find them easily in the literature. Notably the ones from Deserno or Derreumaux. On Oct 10, 2012, at 2:03 PM, rama david wrote: Hi friends, I planed to use the martini force-field for my simulation study of peptide. The peptides are initially alpha-helix in nature. As they come together they formed amyloid fibre( Antiparallel Beta structure). Is it is possible to study the secondary structure backbone study by martini force field. I read in there tutorial that the Secondary structure is predefined therefore they are statics through out the simulation. Conformational changes that produces changes in Sec structure are out of scope in martini. only tertiary structure are free defined to change.. So what to do ??? How to use Martini FF to study secondary structure ??? Is there any way to use coarse grained FF to use for study in Sec. structure??? With Best wishes and regards, Rama David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Martini FF for Sec structure changes...
No, it does NOT! HAve you red the paper?! This implementation is an adoc representation to mimic specific sequences of short peptides! They do never for any secondary structure! On Oct 10, 2012, at 3:05 PM, francesco oteri wrote: Hi rama, actually MARTINI has been further improved to allow secondary structure change. The title is: *Improving Internal Peptide Dynamics in the Coarse-Grained MARTINI Model: Toward Large-Scale Simulations of Amyloid- and Elastin-like Peptides* and here there is a link to the paper: http://dx.doi.org/10.1021/ct200876v Francesco 2012/10/10 XAvier Periole x.peri...@rug.nl Nope, but on other softwares. On Oct 10, 2012, at 2:50 PM, rama david wrote: Thank you for your reply, Are these Cg can be used in Gromacs. Thank you in advance. With best wishes and regards, Rama david On Wed, Oct 10, 2012 at 6:13 PM, XAvier Periole x.peri...@rug.nl wrote: Martini FF cannot model changes in secondary structure ... other CG FF can. You'll find them easily in the literature. Notably the ones from Deserno or Derreumaux. On Oct 10, 2012, at 2:03 PM, rama david wrote: Hi friends, I planed to use the martini force-field for my simulation study of peptide. The peptides are initially alpha-helix in nature. As they come together they formed amyloid fibre( Antiparallel Beta structure). Is it is possible to study the secondary structure backbone study by martini force field. I read in there tutorial that the Secondary structure is predefined therefore they are statics through out the simulation. Conformational changes that produces changes in Sec structure are out of scope in martini. only tertiary structure are free defined to change.. So what to do ??? How to use Martini FF to study secondary structure ??? Is there any way to use coarse grained FF to use for study in Sec. structure??? With Best wishes and regards, Rama David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/ Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use
Re: [gmx-users] Martini lipid bilayer...
Well ... it always depends on what you want to do but the file on the link you give are the official website and they should be reliable :)) On Oct 9, 2012, at 12:04 PM, rama david wrote: Hi Gromacs friends, I am interested in Martini force-field and application in lipid bilayer. I found the lipid bilayer at http://md.chem.rug.nl/cgmartini/index.php/downloads/example-applications/66-dppc-membrane is it is a reliable to use it after more equilibriation ( like 500 ns ) or I have to build my own bilayer Is any other link to get the martini lipids bilayer??? With best wishes and regards, Rama David. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] using martinize.py to martinize two chains complex
You may want to try the forum on rte cgmartini.nl for more ... In short: try martinize.py -h it should give you options to separate the chain topologies. If it does not work that means your chains are not defined as two in the input. Their is not direct manner to CG a lipid file ... the topology is easy to build though ... for the coordinate files you either start from an already existing file or you go through the reverse transformation tutorial. It is mainly used to get atomistic from CG but you can do the inverse ... the steps are identical and most importantly you learn how to build a topology with a mapping section. XAvier. On Sep 5, 2012, at 11:53 PM, Lingyun Wang wrote: Hi all, There are two chains in the complex.pdb file, but martinize.py only recognize them as one chain. What can I do to generate two chains in the complex-martini.top file? My command is as following: python martinize.py -f complex.pdb -o complex-martini.top -x complex-martini.pdb By the way, is any script to generate Martini topology and structure files for lipids available? If not, how can I martinize a lipids bilayer?. Thanks. Lingyun -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] using martinize.py to martinize two chains complex
I believe martinize looks for chain identifiers. There is a column for that in the PDB format. The other solution is to proceed in two steps ... one chain at the time ... On Sep 6, 2012, at 1:22 AM, Lingyun Wang wrote: Hi XAvier, Thank you for your reply. I also tried python martinize.py -f complex.pdb -o complex- martini.top -x complex-martini.pdb -sep, but it still turns out the same result. There is Ter after each chain in the pdb, do I need other way to define that they are two chains? Thanks. Best, Lingyun From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of XAvier Periole [x.peri...@rug.nl] Sent: Wednesday, September 05, 2012 5:52 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] using martinize.py to martinize two chains complex You may want to try the forum on rte cgmartini.nl for more ... In short: try martinize.py -h it should give you options to separate the chain topologies. If it does not work that means your chains are not defined as two in the input. Their is not direct manner to CG a lipid file ... the topology is easy to build though ... for the coordinate files you either start from an already existing file or you go through the reverse transformation tutorial. It is mainly used to get atomistic from CG but you can do the inverse ... the steps are identical and most importantly you learn how to build a topology with a mapping section. XAvier. On Sep 5, 2012, at 11:53 PM, Lingyun Wang wrote: Hi all, There are two chains in the complex.pdb file, but martinize.py only recognize them as one chain. What can I do to generate two chains in the complex-martini.top file? My command is as following: python martinize.py -f complex.pdb -o complex-martini.top -x complex-martini.pdb By the way, is any script to generate Martini topology and structure files for lipids available? If not, how can I martinize a lipids bilayer?. Thanks. Lingyun -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Elastic network model -building
There is no script generating an elastic network in Gromacs. You could use the script that we developed in the context of the Martini CG model (cgmartini.nl) but it would be certainly easier for you to simply write a script that would rad the Clapha coordinates and define the ones that are within a cut-off distance of your choice and then write a list of bonds that you could add to a gromacs topology file ... On Aug 26, 2012, at 3:34 PM, mohan maruthi sena wrote: Hi all, I want to build elastic network model for a protein. To build an Elastic network model , I consider only C-alpha atoms of the protein. I want to make c-alpha atoms connect(make bond) with all the other c-alpha atoms , if it falls within certain cut-off distance. How can i do this? Please suggest me a way, Thanks, Mohan. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Elastic network model -building
On Aug 27, 2012, at 7:14 PM, mohan maruthi sena wrote: Hi, Thanks for your reply. I have written a script which gives the atoms with in certain cut-off distance from specified atom. I have added this to topology , the problem is that it creates topology from pdb but not the other way. Not clear what the other way around is! I use first pdb2gmx -f pdb -o gro -p top (command to generate gro,top). I use this topology file and add the bonds in this and use this topology for further use. Is this correct,? I have no idea! It depends what you want to do! Doing like you describe you add a elastic network to a atomistic description ... if this is not the objective do something that would follow your idea! ,but still i could not find bonds with other atoms when i load it in vmd. Please suggest me a way. VMD defines default bonds according to their distances in the structure you give. So between Calpha the distance is about 0.38 nm ... if you use a dynamic bond description in VMD and select the Calphas ... a cutoff of 4.0 would show you the connections. Thanks, Mohan On Mon, Aug 27, 2012 at 10:29 PM, XAvier Periole x.peri...@rug.nl wrote: There is no script generating an elastic network in Gromacs. You could use the script that we developed in the context of the Martini CG model (cgmartini.nl) but it would be certainly easier for you to simply write a script that would rad the Clapha coordinates and define the ones that are within a cut-off distance of your choice and then write a list of bonds that you could add to a gromacs topology file ... On Aug 26, 2012, at 3:34 PM, mohan maruthi sena wrote: Hi all, I want to build elastic network model for a protein. To build an Elastic network model , I consider only C-alpha atoms of the protein. I want to make c-alpha atoms connect(make bond) with all the other c-alpha atoms , if it falls within certain cut-off distance. How can i do this? Please suggest me a way, Thanks, Mohan. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Comparing amplitudes of motions in two MD simulations
rmsf is what you are looking for. g_rmsf should help. On Jul 14, 2012, at 16:23, Igor Druz idruz...@gmail.com wrote: Hello, I would like to compare amplitude of motion of a specific atom in two sets of MD simulations. Something like rms of displacements about the equilibrium position would do. In your experience, which gromacs analysis tools would be suitable for this? Any other insight into how this can be done best is appreciated. Thank you, Igor -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] MARTINI parameters for dodecyl maltoside (DDM)
Thee are not yet parameters for DDM but indeed the parameters for both the head and the tail are defined separately. It would be very useful to combine them and start building a detergent parameter library ... the topologies would have to be tested against experimental and/or atomistic data. I believe there must be an enormous amount of data on the phase behavior of DDM and other thermodynamic data. On May 21, 2012, at 3:35 PM, Dariush Mohammadyani wrote: Sure, this is the way to make forcefield for your molecule. Also, please check literature. Good luck, Dariush On Mon, May 21, 2012 at 9:26 AM, francesco oteri francesco.ot...@gmail.com wrote: Hi Dariush, I've checked but it seems there no parameters for my detergent. Actully there are parameters for the polar head and the lipidic tail, so it is worth trying to merge them to have the correct representation! Francesco 2012/5/21 Dariush Mohammadyani d.mohammady...@gmail.com Have you checked MARTINI website? http://md.chem.rug.nl/cgmartini/index.php/downloads/force-field-parameters Dariush Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA On Sun, May 20, 2012 at 1:01 PM, francesco oteri francesco.ot...@gmail.com wrote: Dear gromacs users, does someone of you know whether parameters for the detergent dodecyl-beta-maltoside are avalaible in MARTINI forcefield? Thank you in advance, Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] dipole moment
Hi, You do not need to use the polarizable martini water model to calculate the dipole of molecules. Or I am missing a point here! g_dipole should do the work XAvier. On May 13, 2012, at 15:11, dina dusti dinadu...@yahoo.com wrote: Dear Justin, Thank you very much from your response. Best Regards Dina From: Justin A. Lemkul jalem...@vt.edu To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, May 13, 2012 5:23 PM Subject: Re: [gmx-users] dipole moment On 5/13/12 8:41 AM, dina dusti wrote: Dear GROMACS Specialists, I have one system consists of water and two other molecules. I work by MARTINI CG force field. I want to calculate dipole moment of molecules in water. May I ask you to help me, Please? I doubt you can. Unless you are using version 2.P of the force field (which contains polarizable water), MARTINI uses a single, uncharged particle to represent water. If there are no charges, there is no dipole. -Justin -- Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] dipole moment
Interesting ... do you have a reference for this? XAvier. On May 14, 2012, at 12:01 PM, Dommert Florian wrote: On Mon, 2012-05-14 at 09:59 +0200, XAvier Periole wrote: Hi, You do not need to use the polarizable martini water model to calculate the dipole of molecules. Or I am missing a point here! g_dipole should do the work XAvier. Hi, I want to point to another problem. If you simulate with a classical force field, you usually have an effective set of partial charges. This means polarization effects are often included in the partial charges. This in turn requires an appropriate calculation of the dipoles. A simple sum over the charges, like g_dipole or g_current does, is not sufficient. The true dipoles are only obtained, if the results from the MD are multiplied with a certain factor the is related to the high-frequency limit of the dielectric constant, the electronic dielectric constant. We have performed several studies on molecular ionic liquids and showed, that with a set of bulk charges, the dipole moments are reproduced correctly, if this electronic dielectric constant is taken into account appropriate. Also for water or any other molecule, the same arguments hold. For example, if TIP4P water is considered. Calculating the dielectric constant gives a value around 50, which is small compared to the exp. value of 80. However, if the correct dipoles are considered, a simulated value of around 80 is the result. Hence, it depends on the parametrization of the partial charges, how the dipole moment or any related property has to be calculated. If you are just interested in the static limit, an effective description with static partial charges is sufficient in my opinion. However, as soon as you are also interested in the time behavior, like the frequency spectrum of the dielectric constant or conductivity, you consider the electronic polarization explicitly with a corresponding force field, as Justin mentioned. Cheers, Flo On May 13, 2012, at 15:11, dina dusti dinadu...@yahoo.com wrote: Dear Justin, Thank you very much from your response. Best Regards Dina From: Justin A. Lemkul jalem...@vt.edu To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, May 13, 2012 5:23 PM Subject: Re: [gmx-users] dipole moment On 5/13/12 8:41 AM, dina dusti wrote: Dear GROMACS Specialists, I have one system consists of water and two other molecules. I work by MARTINI CG force field. I want to calculate dipole moment of molecules in water. May I ask you to help me, Please? I doubt you can. Unless you are using version 2.P of the force field (which contains polarizable water), MARTINI uses a single, uncharged particle to represent water. If there are no charges, there is no dipole. -Justin -- Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org
Re: [gmx-users] jointly-couple lipids to theromstat - MARTINI force-field
The separation of groups for temperature control is originally necessary to avoid (or correct for) temperature gradient in the system, which occurs when systems parts have different frequencies of motions. Typically the water molecules and a protein would be separated to avoid the freezing of the protein and the heating up of the solvent. It would not make much difference to couple the dppc and dppg lipid groups separately or together. To form a separate group you need a sufficient amount of particle to avoid large (and therefore more difficult to control) fluctuations. Ions are generally coupled to the solvent they are embedded into. Anirban suggestion is fine. On May 3, 2012, at 1:56 PM, Anirban Ghosh wrote: On Thu, May 3, 2012 at 5:17 PM, Weingarth, M.H. m.h.weinga...@uu.nl wrote: Hello, I am a bit confused by a comment which I find in all MARTINI example md.mdp scripts concerning the tc-groups : It is stated there to couple groups separately: MARTINI -Normal temperature and pressure coupling schemes can be used. It ; is recommended to couple individual groups in your system seperately I am simulating a mixed dppc:dppg membrane (see below my parameters). Even these two different lipids-types should be coupled separately? (and how about Na+ (Qd particles) and water - also separately?) I would greatly appreciate any comment on this issue. Thanks a lot Markus my parameter: ; Temperature coupling: tcoupl = berendsen ; Groups to couple separately: tc-grps = DPPC DPPG W NAA Protein Generally in membrane protein simulations different coupling groups are used to increase the accuracy of the calculations (more realistic). In your system you can make make three groups: Protein, Lipids(DPPC+DPPG) and Sol+Ions(Na+Qd) -Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] wham histograms
Not sure but you could compare with unbiased histogram constructed independently. On Apr 23, 2012, at 11:55 AM, Gavin Melaugh wrote: Hi all Are the histograms from histo.xvg (output of g_wham) the biased or unbiased distributions? Cheers Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] martini coarse-grained
Where did you find the topology? On Apr 10, 2012, at 10:44 AM, dina dusti wrote: Dear GROMACS Specialists, I have doubt about definition of tiofen ring in MARTINI CG force field. May I ask you to help me, Please? I defined if as: SC4 and SC5, that SC5 is as S-C-C and SC4 is as C- C. Is it right? Or should I change SC5 to C-S-C for .gro file? And my definition of tiofen in .itp file it is as followed , Please say me that is it right? ;; TIOFEN [moleculetype] ; molname nrexcl TIO 1 [atoms] ; idtyperesnr residu atomcgnrcharge 1 SC4 1 TIO SI1 1 0 2 SC5 1 TIO SI22 0 [constraints] ; i j funct length 1 2 1 0.27 Because I for benzene see a triangle in ngmx program, but for this see a line. Please help me to correction of mistakes. Thank you very much in advance. Best Regards Dina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Exploding Protein with 4.6 and 4.5.5
Try to use constrains = all-bonds which is the way to use Gromos force fields. On Mar 26, 2012, at 12:30, SebastianWaltz sebastian.wa...@physik.uni-freiburg.de wrote: Dear Gromacs user, I try to simulate the human Villin head peace HP35 in approx. 6000 water molecules (spc) with the gromos ff ffG53a6. Using the 4.0.7 version the NPT equilibration for 5ns with position restraint protein (lincs) atoms and a integration step of 0.002 using the leap-frog integrator works just fine. Switching to the 4.5.5 or the 4.6 version with heterogeneous acceleration is leading to an exploding protein after a few ps. Changing the integration time step to 0.0002 delays the explosion for few ps but does not avoid it. The parameters in mdp file for the 4.6 version are the following: ; title= ttt cpp = /lib/cpp include = -I../top constraints = hbonds integrator = md cutoff-scheme= verlet define = -DPOSRES ;constraint_algorithm = shake dt= 0.0002 nsteps = 250 nstcomm= 10 nstxout = 1000 nstvout = 1000 nstfout= 1000 nstlog = 1000 nstenergy = 5000 nstxtcout = 10 xtc_grps= Protein nstlist= 25 ns_type = grid rlist = 1.2 coulombtype = PME rcoulomb= 1.2 vdwtype = cut-off rvdw = 1.2 fourierspacing= 0.12 pme_order = 6 optimize_fft= yes pbc = xyz Tcoupl = v-rescale tc-grps= Protein Non-Protein tau_t = 0.1 0.1 ref_t= 300 300 energygrps = Protein Non-Protein Pcoupl = berendsen tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = all Pcoupltype= isotropic gen_vel = yes gen_temp = 300 gen_seed = -1 Any help is very welcomed. Dears sincerely, Sebastian -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] About martini
Yes unfortunately the transformation is only inplemented in the version available on the martini page. On Mar 9, 2012, at 10:30, francesca vitalini francesca.vitalin...@gmail.com wrote: Either you develop your own version of the mapping or I guess you have to use the old version...sorry, but I'm struggling with it right now and I understand that it can be quite problematic. Francesca 2012/3/9 rama david ramadavidgr...@gmail.com: Dear GROMACS specialists, How to convert Coarse Grain Martini to FG martini on Gromacs 4.5.4 version . ( And how to compile the source given in Martini home page with 4.5.4 version as they mention only Gromacs 3.3.1 version) Please give the valuable advice.. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_fg2cg
Did you define the mapping in the atomistic topology? On Mar 6, 2012, at 10:57, dina dusti dinadu...@yahoo.com wrote: Dear Gromacs Specialists, I have one problem about g_fg2cg. I want convert structure of butanole in fg to cg by g_fg2cg, but I take this error: Program g_fg2cg, VERSION 3.3.1 Source code file: gmxfio.c, line: 735 Range checking error: Variable fio has value -1. It should have been within [ 0 .. 1 ] Please report this to the mailing list (gmx-users@gromacs.org) May I ask you to help me, Please? Thank you very much in advance Best Regards Dina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] antifreeze particle in martini coarse-grained
It was a good idea to ask! You might want to try the MARTINI forum at the cgmartini.nl web site, though. In short the way you did it will probably fill up the box with more water or antifreeze particle than necessary ... As an alternative you may want to simply replace 10% of the existing waters into antifreeze particles. You need to change the name in the gro files and adapt the topology accordingly. Then an equilibration will disperse the WF particle pretty fast. XAvier. On Dec 13, 2011, at 2:56 PM, mohammad agha wrote: Dear Prof. I have a doubt about my way to add antifreeze water to my system, also I think my question looks silly but please help me for more certainty. I changed W to WF in water.gro file of water that I downloaded from MARTINI site and named that antifreezewater.gro , and with below command added antifreeze water to my system: # genbox -cp ---.gro -cs antifreezewater.gro -o .gro - maxsol 1000 Already I had added water.gro to my system with the same command. May I know that I am right or wrong and if I'm wrong please say me the right way? Thanks Best Regards Sara -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] antifreeze particle in martini coarse-grained
You want to keep the conversation in the list so that others may benefit from it. No. You need to place 1 W in the box and manually edit the gro file to change the last 1000 into WF but most importantly in the topology file generate two groups one with 9000 W and the other 1000 WF. Your way may work but the original placement of the WF might be silly. Do not separate the two groups in the mdp file for the temperature control. Leave them together. On Dec 13, 2011, at 4:09 PM, mohammad agha wrote: Dear Prof. Thanks for your reply. Yes, for example if I need 1 water, then I place 9000 water by genbox from water.gro file and 1000 antifreeze water from antifreezewater.gro that I changed W to WF in water.gro and I have in topology file: [ molecules ] solute 100 W9000 wf 1000 Then my way is correct? also I have one group for WF in .mdp and index.ndx files, is it correct? Best Regards Sara From: XAvier Periole x.peri...@rug.nl To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, December 13, 2011 5:34 PM Subject: Re: [gmx-users] antifreeze particle in martini coarse-grained It was a good idea to ask! You might want to try the MARTINI forum at the cgmartini.nl web site, though. In short the way you did it will probably fill up the box with more water or antifreeze particle than necessary ... As an alternative you may want to simply replace 10% of the existing waters into antifreeze particles. You need to change the name in the gro files and adapt the topology accordingly. Then an equilibration will disperse the WF particle pretty fast. XAvier. On Dec 13, 2011, at 2:56 PM, mohammad agha wrote: Dear Prof. I have a doubt about my way to add antifreeze water to my system, also I think my question looks silly but please help me for more certainty. I changed W to WF in water.gro file of water that I downloaded from MARTINI site and named that antifreezewater.gro , and with below command added antifreeze water to my system: # genbox -cp ---.gro -cs antifreezewater.gro -o .gro - maxsol 1000 Already I had added water.gro to my system with the same command. May I know that I am right or wrong and if I'm wrong please say me the right way? Thanks Best Regards Sara -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Martini force field: elastic network
The website has been updated to fit a CG tutorial starting monday in Lausanne. The manner of the construction you describe in your email is not the proper way to do it! The new script is doing it properly. If you want the old script to only generate the elastic network (as it seems from your email) you may have it or use the scripts from the ElNeDyn approach. XAvier. On Oct 14, 2011, at 5:58 PM, Li, Hualin wrote: Dear all, I am using martini force field to generate elastic network for my protein. I generate a list of distance between all beads within a certain distance by: genrestr -f ***.gro -n index.ndx -constr -o constraints getting the constraints.itp file and will continue with the 2nd step by using a script: ./select_restr.pl constraints.itp 0.5 0.9 500 However, the martini forcefield developer seems to update their website yesterday and I can't find the select_restr.pl any more and in the new script they provide ( martinize.py), -elastic to write elastic bonds is not working yet. Could some one provide me the old script select_restr.pl please? Many thanks. ---hualin-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] MARTINI / all-atom mapping
Thanks Justin and Thomas for the helpful comments. Thomas pointed to the example I had in mind. I should have been more specific. It is obvious that we should make the mapping of molecules more easily accessible. Tks for the comments, XAvier. On Aug 30, 2011, at 20:16, Thomas Piggot t.pig...@soton.ac.uk wrote: Hi Mike, If you download the rev_trans.tar.gz archive from the reverse transformation tutorial on the Martini website (http://md.chem.rug.nl/cgmartini/index.php/tutorial/reverse-transformation) the mapping section at the end of the dppc.itp file provides the details of the mapping for this lipid. Cheers Tom On 30/08/11 18:57, Michael Daily wrote: Xavier, I did find the atom2cg.awk script on the downloads- tools of the martini website, but there is no corresponding one for lipids. In any case I can probably figure out the mapping by trial and error, just based on inter-bead distances, but it would be nice to have it officially documented. Mike On Tue, Aug 30, 2011 at 3:06 AM, XAvier Periole x.peri...@rug.nl wrote: it must be some example of mapping lipids on the website: cgmartini.nl On Aug 30, 2011, at 3:55 AM, Michael Daily wrote: Hi all, I am trying to reverse-map some martini lipids to united atom. In order to do this, I'd prefer to have an EXACT definition of the aa-to-cg mapping. I cannot find this, only an imprecise graphic, in the MARTINI paper; the martini.itp file doesn't appear to list which heavy atoms are represented by each CG bead either. For example, I'm looking for something like: 'NC3' : ['C1', 'C2', 'C3', 'N4', 'C5', 'C6'], 'PO4' : ['O7', 'P8', 'O9', 'O10', 'O11','C12'], 'GL1' : ['C13', 'O14', 'C15', 'O16'], 'GL2' : ['C32', 'O33', 'C34', 'O35'], etc. For some atoms it's obvious which MARTINI groups they belong in, but others on the borderline are not obvious. For example, does C12 belong in PO4 or GL1? Anybody have a master list like this? Thanks, Mike -- Michael D. Daily Postdoctoral research associate Pacific Northwest National Lab (PNNL) 509-375-4581 (formerly Qiang Cui group, University of Wisconsin-Madison) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Michael D. Daily Postdoctoral research associate Pacific Northwest National Lab (PNNL) 509-375-4581 (formerly Qiang Cui group, University of Wisconsin-Madison) -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] MARTINI / all-atom mapping
it must be some example of mapping lipids on the website: cgmartini.nl On Aug 30, 2011, at 3:55 AM, Michael Daily wrote: Hi all, I am trying to reverse-map some martini lipids to united atom. In order to do this, I'd prefer to have an EXACT definition of the aa- to-cg mapping. I cannot find this, only an imprecise graphic, in the MARTINI paper; the martini.itp file doesn't appear to list which heavy atoms are represented by each CG bead either. For example, I'm looking for something like: 'NC3' : ['C1', 'C2', 'C3', 'N4', 'C5', 'C6'], 'PO4' : ['O7', 'P8', 'O9', 'O10', 'O11','C12'], 'GL1' : ['C13', 'O14', 'C15', 'O16'], 'GL2' : ['C32', 'O33', 'C34', 'O35'], etc. For some atoms it's obvious which MARTINI groups they belong in, but others on the borderline are not obvious. For example, does C12 belong in PO4 or GL1? Anybody have a master list like this? Thanks, Mike -- Michael D. Daily Postdoctoral research associate Pacific Northwest National Lab (PNNL) 509-375-4581 (formerly Qiang Cui group, University of Wisconsin-Madison) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Fwd: density error bars
You may have wanted to have sent the message to the gmx list! XAvier. Begin forwarded message: From: nicoletta liguori fisico...@gmail.com Date: July 26, 2011 5:28:29 PM MDT (CA) To: x.peri...@rug.nl Subject: density error bars Hi, I'm using Gromacs and its tools to sample some kind of membranes and characterize their features. Actually I don't know what to do about error bars. For example when I calculate the density mass distribution along the axis parallel to the normal to the membrane surface I average on all trajectories using g_density_d on my set contained in the .xtc file. Considering that, for what I understood, it makes the average on time of the density, but without adding any kind of error (there are no possibilities with this tool) I tried to check if there are other tools available to calculate the error bars but seem not to exist!! For example g_analyze reads directly the already averaged set of data (in this case) cause the only possible input is a .xvg file! So I was thinking to (not yet know how, is my first computational trial) to calculate the error with a simple standard deviation (I was thinking to use matlab ), but to do this, I suppose that I have to consider all the points indipendent, and to do this I'd have to look at the autocorrelation function of density itself! but how to do this?? there are again no tools available how do you do when u deal with errors? Thanks for attention and for the help Nicoletta -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] large error bars in PMF
One potential problem you have is that as Justin mentioned your minimum is not well defined and certain much less well sampled than the long distances windows. Small peptides (depends the size) may sample relevant phase space to get reasonable convergence within 8 ns when free in solution; in contact certainly not ... How long is you peptide? You might get a better estimate of your error by plotting all the pmfs you've got through bootstrap (if this is the case) ... and get the errors based on the pmfs aligned on the long distance value and not on the minimum which is probably what you did ... if the minimum is not well defined then it does not make sense. On Jul 21, 2011, at 1:36 PM, Justin A. Lemkul wrote: Rebeca García Fandiño wrote: OK, I will try a dodecahedral box and also to extend my actual simulations. Could you give me some advice about starting to learn about 3D PMF? I have not seen this in the manual, and I have never used it before. I have only found your tutorial about how to calculate PMF in Gromacs 4... In practice, there's basically nothing different between 3D and 1D. You specify the dimensions to which the biasing potential is applied with pull_dim or pull_vec (depending on the pull_geometry used). Right now you're calculating the PMF along the z-dimension only (pull_dim = N N Y), which may be appropriate for one-dimensional processes or those in which the reference group does not rotate much in the timeframe of the sampling. Setting pull_dim = Y Y Y will apply the restraint in all dimensions. -Justin Thanks a lot again for your help. Best wishes, Rebeca. Date: Thu, 21 Jul 2011 15:16:52 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: FW: [gmx-users] large error bars in PMF Rebeca García Fandiño wrote: I am trying to achieve the binding energy of the dimer composed by the two small cyclic peptides, to compare it with experimental. What advantages would I have using 3D PMF instead only 1D for this calculation? Intuitively, two molecules diffuse through solution until they find one another, which to me sounds a lot like a 3D path. Further, using a dodecahedral box for your umbrella sampling removes the problems you're having with the peptides rotating. It sounds like you're trying to pull in one direction along a rectangular box, but the peptides are not playing nice. I feel like this discussion has come up at least once or twice before, though... -Justin Thanks a lot! Rebeca. Date: Thu, 21 Jul 2011 14:14:44 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] large error bars in PMF Rebeca García Fandiño wrote: Hi, thanks a lot for your quick answer. What I am trying to pull are two small peptides one from another (r_1 and r_2). I did not understand very well your last suggestion: ...if you want reasonable error bars you will not lots of well-converged data. Oops, that should have read you will *need* lots of well- converged data. Do you mean I will need also more windows besides extending the simulations? I doubt you need more windows. Likely you just need more time in each. I think the problem could be also that the peptides I am using rotate in the box and they do not remain flat one respect to the other. They gyrate freely and some parts of their structure interact along the pulling... Interactions are part of the dissociation process and are not problematic per se. But if you're trying to obtain only a one-dimensional PMF then your rotation could be a problem. Is there some reason you need a one-dimensional PMF and not a three-dimensional PMF? What are you trying to achieve? -Justin Thanks a lot again for your help. Best wishes, Rebeca. From: rega...@hotmail.com To: gmx-users@gromacs.org Date: Thu, 21 Jul 2011 16:36:59 + Subject: [gmx-users] large error bars in PMF Hi, I am trying to calculate the binding energy of two molecules using the PMF (Umbrella Sampling method) and Gromacs 4.0. Some weeks ago I have written to the list because changing the number of windows used in the Umbrella Sampling calculations different results were obtained, and I was suggested to extend my simulations since the error bars associated to each windows were too high. I have now extended my simulations from 1 ns to 8 ns, however, I cannot see much different from the shorter calculations. I send you the comparison of the two PMF including the error bars (attached). Now I am using 50 windows, but the shorter simulations were done using 100 windows, so I don't think increasing the number of windows could
Re: [gmx-users] large error bars in PMF
Well I do not know how g_wham is doing but it is likely that it does align different pmf obtained through the bootstraap the their minimum. Justin just answered. The other alternative is to inverse your distances with the data files. On Jul 21, 2011, at 2:57 PM, Rebeca García Fandiño wrote: Thanks for your answer. My peptide has 6 residues and it is cyclic. I calculated the errors through bootstrap, using this: g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 500 -n Bootstrap 200 Are the pmfs aligned on the minimum distance value? Is that the value by default? How could I calculate the errors based on the PMFs aligned on the long distance value? Thanks a lot for all the help. Best wishes, Rebeca. From: x.peri...@rug.nl To: gmx-users@gromacs.org Subject: Re: [gmx-users] large error bars in PMF Date: Thu, 21 Jul 2011 14:33:28 -0600 One potential problem you have is that as Justin mentioned your minimum is not well defined and certain much less well sampled than the long distances windows. Small peptides (depends the size) may sample relevant phase space to get reasonable convergence within 8 ns when free in solution; in contact certainly not ... How long is you peptide? You might get a better estimate of your error by plotting all the pmfs you've got through bootstrap (if this is the case) ... and get the errors based on the pmfs aligned on the long distance value and not on the minimum which is probably what you did ... if the minimum is not well defined then it does not make sense. On Jul 21, 2011, at 1:36 PM, Justin A. Lemkul wrote: Rebeca García Fandiño wrote: OK, I will try a dodecahedral box and also to extend my actual simulations. Could you give me some advice about starting to learn about 3D PMF? I have not seen this in the manual, and I have never used it before. I have only found your tutorial about how to calculate PMF in Gromacs 4... In practice, there's basically nothing different between 3D and 1D. You specify the dimensions to which the biasing potential is applied with pull_dim or pull_vec (depending on the pull_geometry used). Right now you're calculating the PMF along the z-dimension only (pull_dim = N N Y), which may be appropriate for one-dimensional processes or those in which the reference group does not rotate much in the timeframe of the sampling. Setting pull_dim = Y Y Y will apply the restraint in all dimensions. -Justin Thanks a lot again for your help. Best wishes, Rebeca. Date: Thu, 21 Jul 2011 15:16:52 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: FW: [gmx-users] large error bars in PMF Rebeca García Fandiño wrote: I am trying to achieve the binding energy of the dimer composed by the two small cyclic peptides, to compare it with experimental. What advantages would I have using 3D PMF instead only 1D for this calculation? Intuitively, two molecules diffuse through solution until they find one another, which to me sounds a lot like a 3D path. Further, using a dodecahedral box for your umbrella sampling removes the problems you're having with the peptides rotating. It sounds like you're trying to pull in one direction along a rectangular box, but the peptides are not playing nice. I feel like this discussion has come up at least once or twice before, though... -Justin Thanks a lot! Rebeca. Date: Thu, 21 Jul 2011 14:14:44 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] large error bars in PMF Rebeca García Fandiño wrote: Hi, thanks a lot for your quick answer. What I am trying to pull are two small peptides one from another (r_1 and r_2). I did not understand very well your last suggestion: ...if you want reasonable error bars you will not lots of well-converged data. Oops, that should have read you will *need* lots of well- converged data. Do you mean I will need also more windows besides extending the simulations? I doubt you need more windows. Likely you just need more time in each. I think the problem could be also that the peptides I am using rotate in the box and they do not remain flat one respect to the other. They gyrate freely and some parts of their structure interact along the pulling... Interactions are part of the dissociation process and are not problematic per se. But if you're trying to obtain only a one-dimensional PMF then your rotation could be a problem. Is there some reason you need a one-dimensional PMF and not a three-dimensional PMF? What are you trying to achieve? -Justin Thanks a lot again for your help. Best
Re: [gmx-users] GPUs and umbrella sampling
Yes, include the harmonic restrain(s) directly into the topology. Then you may convert the info (distance(s), angle(s)) into the g_wham format (which I do not know but should be reasonably easy) or use another script to get your PMF or make you own ... it is possible. On Jul 18, 2011, at 9:37 AM, Guido Polles wrote: Hi everybody, I noticed that GPU version of gromacs do not support the pull code, hence i suppose g_wham cannot be used to extract a PMF. I would like to just ask if somebody could suggest or give any hint about the way to do umbrella sampling and extract a PMF without pull code, so that I will have an idea before I start diving deeper into the issue, make mistakes and potentially write useless code. Thanks in advance for any advice. Guido Polles -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Residence time and trjorder
Mark is right g_dist can help you for this but there is no specific tool calculating residence time ... I guess everyone dreams of someone writing it :)) On Jul 13, 2011, at 2:28 AM, Mark Abraham wrote: On 13/07/2011 5:52 PM, Carla Jamous wrote: Dear Xavier, my problem is the following: I'm trying to figure out if a water molecule is present in a specific area around my protein and if so, which water molecule is that and how long does it stay in that place. I think g_dist does this for a group containing a single water molecule. All you need to do write a script to iterate over each molecule, and then collate the statistics. Mark As you said, if I google residence time, here's the definition: Residence time (also known as removal time) is the average amount of time that a particle spends in a particular system. But I don't find a tool to calculate this residence time in gromacs, so I'm trying to find a trick that can give me a pourcentage of the time of my simulation where a certain water molecule stays in the specific area of my protein. Regards, Carla On Tue, Jul 12, 2011 at 5:51 PM, XAvier Periole x.peri...@rug.nl wrote: Dear Boafu, This sounds like a great tool! Carla, note that once you've ordered the water molecules you loose the continuity of their trajectories ... that is because you order them in function of their distance to the protein. I am not sure the definition you give will give you the answer to the residence time. you can google residence time and proteins and see what come out :)) XAvier. On Jul 12, 2011, at 6:32 AM, Baofu Qiao wrote: HI Carla, I wrote a similar code, see attached. But it is written for my condition. You should modify it accordingly. regards, Baofu Qiao On 07/12/2011 02:04 PM, Carla Jamous wrote: Dear gmx-users, I used trjorder in order to study the water molecules that are closer than 5 A from my protein. trjorder -s structure.tpr -f traj.xtc -n prot_water.ndx -o ordered.pdb -nshell nshell_.xvg -r 0.5 -b 0 -e 5000 But now I need to analyse the residence time of a water molecule, I mean the number of times a single water molecule stays in a radius of 5 A of the protein and divide this number by the total number of conformations, in order to have a pourcentage value. Please is there any gromacs tool able to do this calculation or else does anyone have an idea of how to do that? Thank you Carla g_residence.c-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Residence time and trjorder
Dear Boafu, This sounds like a great tool! Carla, note that once you've ordered the water molecules you loose the continuity of their trajectories ... that is because you order them in function of their distance to the protein. I am not sure the definition you give will give you the answer to the residence time. you can google residence time and proteins and see what come out :)) XAvier. On Jul 12, 2011, at 6:32 AM, Baofu Qiao wrote: HI Carla, I wrote a similar code, see attached. But it is written for my condition. You should modify it accordingly. regards, Baofu Qiao On 07/12/2011 02:04 PM, Carla Jamous wrote: Dear gmx-users, I used trjorder in order to study the water molecules that are closer than 5 A from my protein. trjorder -s structure.tpr -f traj.xtc -n prot_water.ndx -o ordered.pdb -nshell nshell_.xvg -r 0.5 -b 0 -e 5000 But now I need to analyse the residence time of a water molecule, I mean the number of times a single water molecule stays in a radius of 5 A of the protein and divide this number by the total number of conformations, in order to have a pourcentage value. Please is there any gromacs tool able to do this calculation or else does anyone have an idea of how to do that? Thank you Carla g_residence.c-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Problem in followin MARTINI tutorial
Well, there must be some thing some where that you did the wrong way :)) You should try again from the start and may be try to post on the Martini website forum www.cgmartini.nl XAvier On Jun 20, 2011, at 9:41 AM, Naba wrote: Dear Users/Developers I am trying to set a coarse-grained MD for the same protein (1UBQ.pdb) therein the MARTINI tutorial (http://md.chem.rug.nl/cgmartini/index.php/tutorial ). After the solvation by water-1bar-303K.gro I tried to minimize the system but it gives the following weired results. grompp gives the following output: checking input for internal consistency... processing topology... Generated 0 of the 465 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'Protein' Excluding 1 bonded neighbours molecule type 'W' processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... initialising group options... processing index file... Analysing residue names: There are:76Protein residues There are: 5199 Other residues Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Making dummy/rest group for T-Coupling containing 5362 elements Making dummy/rest group for Acceleration containing 5362 elements Making dummy/rest group for Freeze containing 5362 elements Making dummy/rest group for Energy Mon. containing 5362 elements Making dummy/rest group for VCM containing 5362 elements Number of degrees of freedom in T-Coupling group rest is 16053.00 Making dummy/rest group for User1 containing 5362 elements Making dummy/rest group for User2 containing 5362 elements Making dummy/rest group for XTC containing 5362 elements Making dummy/rest group for Or. Res. Fit containing 5362 elements Making dummy/rest group for QMMM containing 5362 elements T-Coupling has 1 element(s): rest Energy Mon. has 1 element(s): rest Acceleration has 1 element(s): rest Freeze has 1 element(s): rest User1has 1 element(s): rest User2has 1 element(s): rest VCM has 1 element(s): rest XTC has 1 element(s): rest Or. Res. Fit has 1 element(s): rest QMMM has 1 element(s): rest Checking consistency between energy and charge groups... This run will generate roughly 2 Mb of data writing run input file... But mdrun gives the following output: Steepest Descents: Tolerance (Fmax) = 1.0e+00 Number of steps= 5000 Step= 14, Dmax= 1.2e-06 nm, Epot= 3.55783e+18 Fmax= inf, atom= 294 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Back Off! I just backed up solvated.gro to ./#solvated.gro.1# Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1. Potential Energy = 3.5578291e+18 Maximum force =inf on atom 294 Norm of force = 1.0627526e+19 Maximum force is equal to infinity and hence I am afraid to proceed further. Can someone help me out? Thanks in advance. Nabajyoti Goswami Senior Research Fellow Bioinformatics Center, Sri Venkateswara College University of Delhi South Campus Benito Juarez Road, Dhaula Kuan New Delhi 110021 India -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Domain Motion = How do get the rotational axis from eigenvectors ?
You should a have good read at the original papers. They are mentioned on the web site. They will answer all your questions. On May 28, 2011, at 6:03, Chih-Ying Lin chihying2...@gmail.com wrote: Hi I want to get the rotational axis about the protein domain motion. From the DynDom website = DynDom is a program to determine domains, hinge axes and hinge bending residues in proteins where two conformations are available. Questions: 1. Do the hinge axes represent the rotational axis about the protein domain motion ? 2. From its User created database, domains and hinge bending residues, rotation angles and translation are created. = The rotation angles must be defined as the angle of rotation between two domains based on the hinge axes, right ? = The vector of the hinge axes is not given by DynDom website, or I did not find it ??? = Hinge axes could be obtained from hinge bending axes residues, right If so, How = How can I get the vector of the hinge axes with the results from DynDom ??? = I found some papers drawing the hinge axes, can Gromacs help me find and draw the hinge axes = From User created database in the DynDom website, it is showing Sequence. What does sequence represent ??? 3. Should I install the program of DynDom and then g_dyndom can be functioned ??? (we need to install DSSP before using do_dssp) 4. From Gromacs manual = The purpose of this program (g_dyndom) is to interpolate and extrapolate the rotation as found by DynDom. What does it mean to interpolate and extrapolate the rotation as found by DynDom ? Thank you Lin Message: 1 Date: Thu, 26 May 2011 19:54:29 -0700 From: Chih-Ying Lin chihying2...@gmail.com Subject: [gmx-users] Domain Motion = How do get the rotational axis fromeigenvectors ? To: gmx-users@gromacs.org Message-ID: banlktinje0fhg6e1dso8aj66_n16xnc...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hi I want to protein's domain motion. I use g_covarandg_anaeig to get the eigenvectors. How can i get the rotational axis of which protein do its domain motion from those eigenvectors? I found the papers and the authors plot its rotational axis of domain motion. How did they make it ? Thank you Lin -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110526/9dde6334/attachment-0001.html -- Message: 2 Date: Fri, 27 May 2011 05:54:07 +0200 From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] Domain Motion = How do get the rotational axis from eigenvectors ? To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: BANLkTinKF=-c5+M7op80Dy2VaFM=ml4...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi Lin, You don't get such axes directly from covariance analysis. If you want to know which rotations are associated with a certain eigenvector, you have to run a routine like dyndom (http://fizz.cmp.uea.ac.uk/dyndom/) on the extreme projections of your trajectory onto an eigenvector. Cheers, Tsjerk -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] decomposing the energy
Two things you have to be careful about: 1- use trr trajectory files. xtc precision is not sufficient and it will give a lot of discrepancies at least for the bonded terms. 2- set the nstlist to 1 as the neiboring list should be undated for each frame and not every 5/10 as it is normally set in a regular mdp file. On May 14, 2011, at 1:11 PM, Justin A. Lemkul wrote: Ramachandran G wrote: Hello gmx users: I did 1ns simulation for my system and have the trajectory and energy files. Now i want to see the energy of some specific residues. So, i decompose(separated) the energy groups and edited the mdp file. Using the mdp file, i created a new tpr file and rerun the mdrun using the trajectory file. But when i compared the total energy between the old and new one, it differs a lot. I am doing some mistakes somewhere. Can anyone help me please. Thanks. Maybe, maybe not. Without seeing the .mdp settings and the data that you're looking at, all anyone can do is guess. You also haven't stated what type of trajectory (i.e. .xtc or .trr) you're using as -rerun input. If you're using an .xtc file, there is no velocity information, so any property related to velocities (most notably kinetic energy, but several others as well) will be zero. I suspect this is probably where the discrepancy is, but it is not a problem. Using energygrps is only useful for decomposing short- range nonbonded energy terms, nothing else. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Surface area calculation
reference: Eisenhaber F, Lijnzaad P, Argos P, Sander C, Scharf M (1995) J. Comput. Chem. 16, 273-284. On May 11, 2011, at 2:34 PM, Laura Leay wrote: Can anyone explain in detail the method that gromacs uses to calculate surface area? Which surface area is it calculating (e.g., connolley, accessible)? I am under the impression that the final result is given in nm^2. Is this correct? Carrying out the surface area calculation in gromacs using the OPLS all atom force field I obtain a value of 4.43 nm^2 for methane (carbon = opls_138, sigma = 0.35 and hydrogen = opls_140, sigma = 0.25) (CT-HC ideal bond length = 0.109, e=284512). The command was g_sas -f conf.gro -s topol.tpr -oa -or -tv -probe 0.2 -ndots 200 - nopbc and the result was taken from resarea.xvg I have written a program to calculate the geometric accessible surface area using the van der waals radius of the atoms and a probe of a given size. The surface is defined from the centre of the probe. Using the above values for sigma I obtain a value for methane of 1.15 nm^2 with a probe diameter of 0.2 nm. Obviously the two do not match and I am not sure why. The individual atom areas for my molecule are: C 0.22 H 0.24 H 0.23 H 0.22 H 0.24 Attached are the files used in the gromacs calculation along with the output and my own program. If any one has any suggestions please let me know. area .xvg atomarea .xvg conf .gro grompp.mdpmethane.itpresarea.xvgtopol.topPIsurfaceOPLS.f90-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella sampling
On Mar 31, 2011, at 11:53 AM, Gavin Melaugh wrote: Hi All I have generated several PMF curves for the one system using umbrella sampling. In the first part of the curve (barrier region) I use a high force constant with small intervals between the windows. The latter part of the curve I use a lower force constant with larger window spacing. Anyway I have a few issues that I need clarifying: 1 - Can you have too much overlap between windows? no, there no such a thing of too much overlap :)) You could even put two identical windows with same 100% overlap ... no problem. 2 - Does the distribution at each window have to centered around the desired r0? (If not does this affect the free energy?) The deviation of the distribution from the r0 is what dictates the profile. The more away from the disired r0 the higher the free energy of the system. 3- If you over sample one particular window, will it affect the curve? There is no such a thing of over sampling ... the only thing you can have is not enough sampling. Many thanks GAvin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella sampling
You can present the data differently: you have two windows at 0.78 nm giving different distribution. That indicates these windows are not converged. Does not mean that the others (0.80 nm) are converged :)) On Mar 31, 2011, at 12:20 PM, Gavin Melaugh wrote: Hi Xavier Thanks for the reply. With respect to your answer of my first query. What if you had two windows practically on top of each other, but one was not supposed to be there. e.g A window with r0 of 0.80 nm and centred at 0.78 nm and a window with r0 of 0.78 nm centred at 0.78nm. Gavin XAvier Periole wrote: On Mar 31, 2011, at 11:53 AM, Gavin Melaugh wrote: Hi All I have generated several PMF curves for the one system using umbrella sampling. In the first part of the curve (barrier region) I use a high force constant with small intervals between the windows. The latter part of the curve I use a lower force constant with larger window spacing. Anyway I have a few issues that I need clarifying: 1 - Can you have too much overlap between windows? no, there no such a thing of too much overlap :)) You could even put two identical windows with same 100% overlap ... no problem. 2 - Does the distribution at each window have to centered around the desired r0? (If not does this affect the free energy?) The deviation of the distribution from the r0 is what dictates the profile. The more away from the disired r0 the higher the free energy of the system. 3- If you over sample one particular window, will it affect the curve? There is no such a thing of over sampling ... the only thing you can have is not enough sampling. Many thanks GAvin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella sampling
My bad, I red to quick and though you had three windows ... you should follow Justin's advice. On Mar 31, 2011, at 2:20 PM, Gavin Melaugh wrote: Thanks Justin for the reply Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Sorry I am not sure that I follow. Will the window with r0 =0.80 giving the distribution centred around 0.78nm not drive my free energy profile up. If I remove this window prior to running g_wham the free energy goes down. Should I increase the force constant so that the mean of the window is 0.80nm (bearing in mind that this is near the barrier region). If you have an incomplete or otherwise discontinuous free energy profile, then you won't get a correct result, but it's not simply due to oversampling one region. It's that the oversampling results in undersampling another region. Increasing the force constant for the window centered around 0.80 nm should work. -Justin Gavin XAvier Periole wrote: You can present the data differently: you have two windows at 0.78 nm giving different distribution. That indicates these windows are not converged. Does not mean that the others (0.80 nm) are converged :)) On Mar 31, 2011, at 12:20 PM, Gavin Melaugh wrote: Hi Xavier Thanks for the reply. With respect to your answer of my first query. What if you had two windows practically on top of each other, but one was not supposed to be there. e.g A window with r0 of 0.80 nm and centred at 0.78 nm and a window with r0 of 0.78 nm centred at 0.78nm. Gavin XAvier Periole wrote: On Mar 31, 2011, at 11:53 AM, Gavin Melaugh wrote: Hi All I have generated several PMF curves for the one system using umbrella sampling. In the first part of the curve (barrier region) I use a high force constant with small intervals between the windows. The latter part of the curve I use a lower force constant with larger window spacing. Anyway I have a few issues that I need clarifying: 1 - Can you have too much overlap between windows? no, there no such a thing of too much overlap :)) You could even put two identical windows with same 100% overlap ... no problem. 2 - Does the distribution at each window have to centered around the desired r0? (If not does this affect the free energy?) The deviation of the distribution from the r0 is what dictates the profile. The more away from the disired r0 the higher the free energy of the system. 3- If you over sample one particular window, will it affect the curve? There is no such a thing of over sampling ... the only thing you can have is not enough sampling. Many thanks GAvin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] GROMACS 4.5 and MARTINI Force Field Installation
You can use any GROMACS version to run a simulation with the Martini Force field. IT is only if you want to back-map your system to an atomistic resolution that you'll have to use the gmx331 modified version. On Mar 27, 2011, at 8:25 PM, Edroaldo Lummertz da Rocha wrote: Dear GROMACS users, I am starting to setup a molecular dynamics simulation and I want to use the MARTINI force field. I was reading the tutorial in website: http://md.chem.rug.nl/cgmartini/index.php/tutorial/reverse-transformation and I have a beginner question for you: How can I use the MARTINI in the GROMACS 4.5? I ask that because the link above provides a modified version of GROMACS to perform the mappings between Fine Grained and Coarse Grained structures. However, the package provided is the GROMACS 3.3.1 version and I don't want to change my GROMACS version. I search in CCL and GROMACS mailing list about this and I didn't find how to do that. Can you help me? Thanks so much. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] calcium diffuses away from the protein during MD
It is unfortunately often that cations on their binding sites in proteins are not stable. Either the site reorganize or the ion leaves. The problem is that ions parameters and especially double charged ones are difficult to parameterize. It is often that people use additional restrains (harmonic bonds, weak compared to regular ones) to maintain the ion bound. XAvier On Mar 4, 2011, at 6:55, Sunita Patel sun...@mailhost.tifr.res.in wrote: Dear Users, I performed MD simulation on a calcium binding protein with bound calcium starting from the crystal structure using gromos96 forcefield with explicit solvent with NVT ensembles. I performed energy minimization of calcium bound protein with water and following this position restraint molecular dynamics was performed. Subsequently, MD was performed on the system. In a less than 100 ps the calcium ion diffuse away from protein. However, in the experiment (NMR and X-ray)the protein is stable in calcium bound form. What could be the reason for this? How can this problem be fixed? Thanks. Sunita -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] negative steps from tpbconv
Hi Jesper, This occurs when you ask for a number of steps that exceed the the size of an integer! I got the same problem recently ... The only solution I found was to make a new mdp file where t0 is the old time and asking for the extension you need ... you can give trr and edr files to grompp so the tpr file is a continuation of earlier one ... XAvier. On Feb 24, 2011, at 11:50 AM, Jesper Sørensen wrote: Hi, I am trying to extend the run time in tpr file to include more steps using tpbconv… This has worked well for a while, but now I get two errors… One is that it writes “now -207466 steps”, which doesn’t make sense – why is this number negative… Also, “You've simulated long enough. Not writing tpr file” If I extend the simulation using the –nsteps flag, then it will write the tpr file, but still comes up with negative numbers whens starting mdrun with the file, which mdrun does not exactly like. Output is a s follows: READING COORDS, VELS AND BOX FROM TRAJECTORY ../ T305/512DPPC_9728W_305K_625ns.trr... trn version: GMX_trn_file (single precision) Readtrr frame 4166: step 212466 time 53116500.000 Using frame of step 212466 time 5.31165e+07 Extending remaining runtime of by 625000 ps (now -207466 steps) You've simulated long enough. Not writing tpr file Best regards, Jesper -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] negative steps from tpbconv
I am not sure the use of cpt would work! I might have tried and got a problem since the cpt might define where it is going (nsteps) ... to be tried! @Tsjerk: I have not been able to use the nsteps set to -1 for some reason it was telling it had ran enough! Any idea why would that be? On Feb 24, 2011, at 1:01 PM, Tsjerk Wassenaar wrote: Hi Jesper, Using a .cpt file will also work with the modified .tpr file. Maybe it is also worth considering using the -maxh option to mdrun, with nsteps in the .mdp file set to -1 (run infinitely). That avoids the hassle with extensions. Cheers, Tsjerk 2011/2/24 Jesper Sørensen li...@jsx.dk: Hi Xavier, That worked, thanks… Would it also work if I just gave the old state.cpt file to mdrun? Jesper From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org ] On Behalf Of XAvier Periole Sent: 24. februar 2011 12:19 To: Discussion list for GROMACS users Subject: Re: [gmx-users] negative steps from tpbconv Hi Jesper, This occurs when you ask for a number of steps that exceed the the size of an integer! I got the same problem recently ... The only solution I found was to make a new mdp file where t0 is the old time and asking for the extension you need ... you can give trr and edr files to grompp so the tpr file is a continuation of earlier one ... XAvier. On Feb 24, 2011, at 11:50 AM, Jesper Sørensen wrote: Hi, I am trying to extend the run time in tpr file to include more steps using tpbconv… This has worked well for a while, but now I get two errors… One is that it writes “now -207466 steps”, which doesn’t make sense – why is this number negative… Also, “You've simulated long enough. Not writing tpr file” If I extend the simulation using the –nsteps flag, then it will write the tpr file, but still comes up with negative numbers whens starting mdrun with the file, which mdrun does not exactly like. Output is a s follows: READING COORDS, VELS AND BOX FROM TRAJECTORY ../T305/512DPPC_9728W_305K_625ns.trr... trn version: GMX_trn_file (single precision) Readtrr frame 4166: step 212466 time 53116500.000 Using frame of step 212466 time 5.31165e+07 Extending remaining runtime of by 625000 ps (now -207466 steps) You've simulated long enough. Not writing tpr file Best regards, Jesper -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Can g_wham support using different temperature for different windows?
On Feb 23, 2011, at 3:21 AM, Jianguo Li wrote: Thank you for the the useful information, XAvier. My peptide is highly positively charged, 18 AA with +12 charges. Other of my group members told me their NMR experiment in water indicates the peptide conformation is very dynamics. Actually I also did peptide refolding using REMD in water, and I found it is flexible and has no stable structure in water, except some instantaneously helical structures. In addition, my peptide consists of two branches connected by unnatural peptide bond, so the backbone is discontinuous, and also because of the high charges, I assume the peptide doesn't form helcial structure in the negatively charged membrane. Therefore I didn't put any constraints in the peptide to keep the secondary structure of the peptide. I know there are assumptions in my model, but I have no other information to increase the accuracy of the model. In fact, when I am doing REMD folding simulations using Gromos53a6 and CHARMM27 with cMap, I got different results. But the common thing is that both results seems to indicate the peptide is filexbile in water without stable secondary structure. Then I used MARTINI FF with flexible structure, just to find some general features. I will try your suggestion, doing REMD in those bad windows. And the reference you mentioned is very useful, I will take a look at them :-) Another question: Suppose some other tools support using different temperatures in different windows, as you mentioned, if 500K is too high to have a significant contribution to the probability of 300K, can I do a series of simulation in a certain window with different temparatures (e.g. 300K, 350K, 400K,450K, 500K). In such cases, in each window, I need to do 5 simulations, which will be much cheaper than doing REMD in that window. It would be computationally cheaper but this is assuming that you'd get the info you are looking for within these simulations and again the weight of the conformations from 400/450/500 K at 300 K is questionable. Note also that the conformations sampled at high temperature with position restrains on the lipids to avoid deformation will be difficult to interpret! Cheers Jianguo From: XAvier Periole x.peri...@rug.nl To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, 22 February 2011 21:18:12 Subject: Re: [gmx-users] Can g_wham support using different temperature for different windows? A few notes: - the original method (Kumar-JCC-1992) that inspired wham was actually developed to mix different temperature simulations. It is however not clear for the type of system you are simulating how much a 500K simulation would be useful to improve the sampling at 300 K or so. The reason is that the enthalpy difference between the two systems is so high that the probability that a conformation from a 500K simulation would contribute to sampling at 300K is really low. It would much more efficient for systems with implicit solvent for which the energy of the system does not vary so much with the temperature. One could look at Chodera-JCTC-2007 and ref therein for a few examples. - I would think that a REMD simulation would be more useful. No need to run 30 replicas to very hight temperature! A bilayer at 500K might get funny. - Martini force field for flexible regions of protein should not be trusted ... or really interpreted with a lot of reserve. The coil definition is simply something flexible with absolutely no guaranty that it could be representing some thing even close to reality, which we have only an approximate idea of what it is! - A peptide in a bilayer has a very high chance to get into a helical conformation. Do you think it is reasonable to keep it flexible? - As noted by Justin and Chris, you definitely have a problem of convergence ... I am not sure how many converged examples of PMFs of peptide crossing a bilayer are out in the literature (Justin?) but from our experience with Martini it does take an awful lot of time to really get convergence. For you system I would expect at least a microsecond for the windows where sampling is an issue. As an example, we saw significant differences on a PMF between two simple helices up to 8 us ... and no charges were involved. This might be a lot pessimistic but you should not get fooled by a CG model. Martini is really good for a lot of things but other things should really but be looked at carefully. XAvier. On Feb 22, 2011, at 9:12 AM, Jianguo Li wrote: Sorry I forgot to attach my mdp files. Here is the mdp file for pulling simulaition: - -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't
Re: [gmx-users] Can g_wham support using different temperature for different windows?
A few notes: - the original method (Kumar-JCC-1992) that inspired wham was actually developed to mix different temperature simulations. It is however not clear for the type of system you are simulating how much a 500K simulation would be useful to improve the sampling at 300 K or so. The reason is that the enthalpy difference between the two systems is so high that the probability that a conformation from a 500K simulation would contribute to sampling at 300K is really low. It would much more efficient for systems with implicit solvent for which the energy of the system does not vary so much with the temperature. One could look at Chodera-JCTC-2007 and ref therein for a few examples. - I would think that a REMD simulation would be more useful. No need to run 30 replicas to very hight temperature! A bilayer at 500K might get funny. - Martini force field for flexible regions of protein should not be trusted ... or really interpreted with a lot of reserve. The coil definition is simply something flexible with absolutely no guaranty that it could be representing some thing even close to reality, which we have only an approximate idea of what it is! - A peptide in a bilayer has a very high chance to get into a helical conformation. Do you think it is reasonable to keep it flexible? - As noted by Justin and Chris, you definitely have a problem of convergence ... I am not sure how many converged examples of PMFs of peptide crossing a bilayer are out in the literature (Justin?) but from our experience with Martini it does take an awful lot of time to really get convergence. For you system I would expect at least a microsecond for the windows where sampling is an issue. As an example, we saw significant differences on a PMF between two simple helices up to 8 us ... and no charges were involved. This might be a lot pessimistic but you should not get fooled by a CG model. Martini is really good for a lot of things but other things should really but be looked at carefully. XAvier. On Feb 22, 2011, at 9:12 AM, Jianguo Li wrote: Sorry I forgot to attach my mdp files. Here is the mdp file for pulling simulaition: - -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] removing pbc jumps from trajectory
You have to make sure of two things: 1- use a reference (gro or tpr) where the molecule is whole! The tpr is prefered since the molecules are defined. 2- with such a reference and the option -mol you'll get a trajectory with the protein as a whole. On that trajectory you may apply more modifications: -nojump with generate a trajectory where the pbc are not applied so you can do msd analysis. Note that thisnis done by default in g_msd. - fitting with only translation removed (equivalent to centering but more stable. Centering works strangely) XAvier. On Feb 21, 2011, at 8:52, Evelyne Deplazes depla...@student.uwa.edu.au wrote: Hi I have a series of trajectories from a coarse grained simulation (Martini force field) that I ran using gromacs 4.0.4. The system consists of a protein embedded in a POPC bilayer solvated with water. During the simulation the protein (most of time its actually *part* of the protein) jumps across the pb into the neighboring box. I use a series of tcl scripts to analyse my trajectories and for that purpose I need to remove that period boundary jump and make the protein whole again. I have tried the approach described on the gromacs website http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions I also other combinations of -whole, -center and -pbc nojump of trjconv, without any luck. Can anyone suggest how I can re-center the protein and remove the pb jump ie make the protein whole Thanks Evelyne -- Evelyne Deplazes PhD student Theoretical Chemistry group University of Western Australia -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: gmx-users Digest, Vol 82, Issue 150
ok this does not make sense! Did you check your tpr file? the command 1) should give you a trajectory where the molecules are whole but jumping across the boundaries ... if it does not that means that the tpr is fucky! Try to visualize your tpr in vmd ... night give you some insight on what is going on! You could also make a tpr file ... making sure things a fine :)) On Feb 21, 2011, at 9:45 AM, Evelyne Deplazes wrote: I tried a couple of things according to your suggestions, but no luck so far I used the following commands 1) trjconv -f trajout_dt2000.xtc -s topol.tpr -pbc mol -o trajout_mol.xtc 2) trjconv -f trajout_mol.xtc -s topol.tpr -pbc nojump trajout_nojump.xtc no luck...If I use command 1) only the trajout_mol.xtc the protein is still split into to across 2 boxes ie it looks like it did not do anything to the trajectory if I use 1) and 2) the system gets ripped apart. The system is no longer a box but a flat disk (very funky) then I tried trjconv -f trajout_dt2000.xtc -s topol.tpr -pbc mol -fit translation -o trajout_fit.xtc again...it looks like the trajectory did not change and the protein is still jumping out of the box then I tried trjconv -f trajout_dt2000.xtc -s topol.tpr -pbc mol -trans -6 6 0 - o trajout_trans.xtc(the box is about 12 x 12) now at least this command did something to the trajectory. The entire protein is now in the center of the box (rather than in the corner) but in the frames where the pb jump occurs the protein still jumps out of the box! it now simply jumps from the center to the next box rather than sliding across the border into the next box On 21 February 2011 16:02, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: g_covar to calculate correlation of motion (Tsjerk Wassenaar) 2. Re: g_covar to calculate correlation of motion (bipin singh) 3. removing pbc jumps from trajectory (Evelyne Deplazes) 4. Re: removing pbc jumps from trajectory (XAvier Periole) -- Forwarded message -- From: Tsjerk Wassenaar tsje...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Mon, 21 Feb 2011 08:14:26 +0100 Subject: Re: [gmx-users] g_covar to calculate correlation of motion Hi Bipin, Try using a .gro or .pdb file as reference structure (-s). Only .tpr files are version specific. Cheers, Tsjerk On Feb 21, 2011 8:05 AM, bipin singh bipinel...@gmail.com wrote: Dear GMX users, I want to calculate the correlated motion between atoms during the md simulation for that purpose I am using g_covar(the one which is available under http://www.gromacs.org/Downloads/User_contributions/Other_software) but it is not compatible with the GROMACS-4.5.3, so please suggest me the alternative way or does anyone have the modified g_covar for GROMKACS-4.5.3. -- - Thanks and regards Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Forwarded message -- From: bipin singh bipinel...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Mon, 21 Feb 2011 13:17:48 +0530 Subject: Re: [gmx-users] g_covar to calculate correlation of motion Hi, Thanks for your suggestion. While running the g_covar it is showing the error that aminoacids.dat is not found, so i have copied the residuetypes.dat(which i seems the new modified name for aminoacids.dat in current GROMACS version), then it prompts to choose the group for least square fit, which is not usual groups(i.e protein or C alpha groups etc.).please suggest where i have made mistake. Choose a group for the least squares fit Opening library file aminoacids.dat WARNING 2 [file aminoacids.dat, line 1]: File aminoacids.dat is empty Group 0 ( System) has 30585 elements Group 1 ( GLU) has47 elements Group 2 ( HIS) has86 elements Group 3 ( ASN) has 224 elements Group 4 ( PRO) has56 elements Group 5 ( VAL) has 272 elements Group 6 ( MET) has68 elements Group 7 ( GLY) has 168 elements Group 8 ( ILE) has
Re: [gmx-users] how many contacts has a certain atom at MD
g_dist On Feb 21, 2011, at 11:32 AM, Olga Ivchenko wrote: Dear Gromacs Users, I would like to know if there is in gromacs an option how to calculate how many contacts has a certain atom i(n a molecules of interest) with water during the whole MD simulations (or at each step of MD). Please could you advice me on this? best, Olga -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulation using Martini force field
Dear Regina, You have two problems: 1- the parameterization of phosphorylated serine should be done following the same philosophy of Martini. Check the Martini papers to see how this is done. In short partitioning is of primary importance. 2- you want to simulate unfolded protein ... indeed there is evidently no persistent structure in such system and therefore the choice for secondary structure would be coil in the Martini force field. However the definition of coil for Martini has not been parameterize to reproduce anything even close to what an unfolded protein, assuming that we know what it looks like :)) The Martini coil is simply something flexible. I am afraid Martini is just not ready for simulating unfolded proteins. Any outcome of a simulation would have to be interpreted with CARE! XAvier. On Feb 14, 2011, at 2:09 PM, pol...@fh.huji.ac.il wrote: Dear Gromacs users and developers, I'm interested to run simulation of natively unstructured protein (casein), that can self assembly and create micelles, using Martini force field. The initial structure of the monomer was created and minimized using Sybyl. This protein includes also 4 phosporylated serines. I'm trying to understand how should I set my system. I started from the tutorial (http://md.chem.rug.nl/cgmartini/index.php/tutorial/ubiquitin-in-water ) but I found that have no idea how to create a phosphorylated serine inCG structure (I have it in my initial pdb). In addition, I found that I need a secondary structure of the protein and I don't have something like this. Moreover, this protein doesn't have one. I will appreciated very much if somebody can help me and guide me a little. Thank you very much in advance. Regina This message was sent using IMP, the Internet Messaging Program. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulation using Martini force field
On Feb 14, 2011, at 7:24 PM, devicerandom wrote: On 14/02/11 13:42, XAvier Periole wrote: Dear Regina, You have two problems: 1- the parameterization of phosphorylated serine should be done following the same philosophy of Martini. Check the Martini papers to see how this is done. In short partitioning is of primary importance. 2- you want to simulate unfolded protein ... indeed there is evidently no persistent structure in such system and therefore the choice for secondary structure would be coil in the Martini force field. However the definition of coil for Martini has not been parameterize to reproduce anything even close to what an unfolded protein, assuming that we know what it looks like :)) The Martini coil is simply something flexible. I am afraid Martini is just not ready for simulating unfolded proteins. Any outcome of a simulation would have to be interpreted with CARE! Agree with Xavier. I am working exactly on a coarse grained generic FF that could allow this kind of simulations, but it's far from being production ready -not an easy task at all. :) thanks for your support devicerandom! XAvier. On Feb 14, 2011, at 2:09 PM, pol...@fh.huji.ac.il wrote: Dear Gromacs users and developers, I'm interested to run simulation of natively unstructured protein (casein), that can self assembly and create micelles, using Martini force field. The initial structure of the monomer was created and minimized using Sybyl. This protein includes also 4 phosporylated serines. I'm trying to understand how should I set my system. I started from the tutorial (http://md.chem.rug.nl/cgmartini/index.php/tutorial/ubiquitin-in-water ) but I found that have no idea how to create a phosphorylated serine inCG structure (I have it in my initial pdb). In addition, I found that I need a secondary structure of the protein and I don't have something like this. Moreover, this protein doesn't have one. I will appreciated very much if somebody can help me and guide me a little. Thank you very much in advance. Regina This message was sent using IMP, the Internet Messaging Program. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- http://devicerandom.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulation using Martini force field
On Feb 14, 2011, at 11:43 PM, pol...@fh.huji.ac.il wrote: Thank you very much for you reply. Can you please explain me why do i need secondary structure file at all and why secondary structure is pre-defined and thus static throughout a simulation? I didn't see that something like this defined for lipids. Have look at the Martini paper for protein (JCTC-2009) you might find some stuff quite instructive in there :)) FYI lipids do not have secondary structure or something that would succgest they could have different interacting behavior in function of their conformation. How do I use do_dssp to build the needed file? I saw that I need a topology file in rder to use do_dssp. Where can I find this topology file? I hope this is ok that I'm asking so many questions. Thank you very much for your help. No problem it just shows how it was a good idea to make a tutorial :)) have look there cgmartini.nl Regina Quoting XAvier Periole x.peri...@rug.nl: Dear Regina, You have two problems: 1- the parameterization of phosphorylated serine should be done following the same philosophy of Martini. Check the Martini papers to see how this is done. In short partitioning is of primary importance. 2- you want to simulate unfolded protein ... indeed there is evidently no persistent structure in such system and therefore the choice for secondary structure would be coil in the Martini force field. However the definition of coil for Martini has not been parameterize to reproduce anything even close to what an unfolded protein, assuming that we know what it looks like :)) The Martini coil is simply something flexible. I am afraid Martini is just not ready for simulating unfolded proteins. Any outcome of a simulation would have to be interpreted with CARE! XAvier. On Feb 14, 2011, at 2:09 PM, pol...@fh.huji.ac.il wrote: Dear Gromacs users and developers, I'm interested to run simulation of natively unstructured protein (casein), that can self assembly and create micelles, using Martini force field. The initial structure of the monomer was created and minimized using Sybyl. This protein includes also 4 phosporylated serines. I'm trying to understand how should I set my system. I started from the tutorial (http://md.chem.rug.nl/cgmartini/index.php/tutorial/ubiquitin-in-water ) but I found that have no idea how to create a phosphorylated serine inCG structure (I have it in my initial pdb). In addition, I found that I need a secondary structure of the protein and I don't have something like this. Moreover, this protein doesn't have one. I will appreciated very much if somebody can help me and guide me a little. Thank you very much in advance. Regina This message was sent using IMP, the Internet Messaging Program. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists This message was sent using IMP, the Internet Messaging Program. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] WHAM with multiple force constants
On Feb 10, 2011, at 3:08 PM, jk...@ifr88.cnrs-mrs.fr wrote: Hi, I'm running an Umbrella Sampling analysis, with 1A steps in the reaction coordinate (distance) to estimate a PMF. However, owing to (high?) energetic barriers between my two proteins, some coordinates are not sampled. I intend to run simulations with stronger force constants to prevent my protein from fleeing to the nearest energetic minima. So my question is : does using different force constants to restrain the distance between my two proteins influences the PMF estimated by g_wham ? No it does not assuming each window is equilibrated. From what I understood, it doesn't seems so, as long as the distributions are well overlapped. But since I intend to invest a considerable amount of CPU time, a confirmation would be really apreciated ! Thanks, Jonathan. -- Message envoyé via le Webmail de l'IFR88 (http://www.ifr88.cnrs- mrs.fr). -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Sampling windows
On Jan 5, 2011, at 4:08 PM, Gavin Melaugh wrote: Dear all I have generated a PMF curve for introducing a guest molecule into a host molecule using the umbrella sampling method. The curve seems fine, but there are no overlaps between histograms in the barrier region. To circumvent this I have added more windows in this region and to ensure sampling have increased the force constant only in this region. The windows in this problematic region are now not equally spaced. Does this matter for g_WHAM? Nope it does not matter. Could someone please reply to me on this matter as it has been a sticking point for me for quite sometime? Many thanks Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Sampling windows
On Jan 5, 2011, at 5:01 PM, Gavin Melaugh wrote: Hi Xavier Many thanks for the reply. When I compare the two curves Curve 1) lack of overlap in barrier region; force constant = 1000 Curve 2) with increased number of sampling windows with increased force constant (note I have only increased the force constant of the windows in the barrier region). Force constant =1000, Force constant in barrier region = 5000 The barrier increases due to better sampling in this region (expected), but the rest of the curve in 2) is shifted upward compared to curve 1). Why is this so when the only difference is the increased number of windows and force constant in one region? the relative position of the regions on the left and right of your barrier region is completely depending on the barrier region! you may have overestimated the difference between bound/unbound states because the energy barrier region was not sampled. Note also that cure one is simply wrong so comparing to it is dangerous. You have to be careful that you might still not have a converged sampling: you might have overlap of your histograms on the reaction coordinate but other degrees of freedom are not fully sampled ... that might result in a funny and wrong profile. You might want to look at your simulations for funny things ... Gavin XAvier Periole wrote: On Jan 5, 2011, at 4:08 PM, Gavin Melaugh wrote: Dear all I have generated a PMF curve for introducing a guest molecule into a host molecule using the umbrella sampling method. The curve seems fine, but there are no overlaps between histograms in the barrier region. To circumvent this I have added more windows in this region and to ensure sampling have increased the force constant only in this region. The windows in this problematic region are now not equally spaced. Does this matter for g_WHAM? Nope it does not matter. Could someone please reply to me on this matter as it has been a sticking point for me for quite sometime? Many thanks Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
