Re: [gmx-users] Regarding g_order
Thanks Justin for the quick reply. I am simulating a protein with bound lipids. I am in a dilemma to choose the direction of the normal to calculate order parameter. In your *Membrane-protein *simulation tutorial, you have chosen normal to the bilayer along the z-axis. But in my case, there is no bilayer, infact, only few bound lipids are there. In which direction I should choose the normal (*-d option*)? On Thu, Aug 1, 2013 at 10:54 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/1/13 12:07 PM, Venkat Reddy wrote: Dear Gmx-users, In the GROMACS site, it has been mentioned that there is a bug (Instead of numbering carbons from 2-17, the numbering starts from 1-16) in g_order program up to, and including, v4.5.4. But when I am using v4.5.5, I am getting the same sort of numbering. Is it normal or I should renumber from 2-17? If you're getting a number starting with 1, it's probably wrong. You can't calculated Scd for the first carbon in a chain because there is no n-1 carbon from which to determine the necessary vectors. Someone (probably me) updated the wiki when version 4.5.4 was current, so probably any 4.5.x version is really affected, and 4.6.x may be as well, since this really is just a trivial bug that requires simple reinterpretation. -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 -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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] remd
Sir, I did an 80 ns Remd simulation, after completion of the simulation extended it up to 480 ns using tpbconv. Now the extended trajectories also write on old trajectory files(traj.trr)? -- 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] Gromacs: GPU detection
Hi there. Lately I've been running simulations using GPUs on a computer node. I noticed that though the GPUs are always in use sometimes I don't get this message in the output: Using 4 MPI threads Using 2 OpenMP threads per tMPI thread 4 GPUs detected: #0: NVIDIA Tesla C2070, compute cap.: 2.0, ECC: yes, stat: compatible #1: NVIDIA Tesla C2070, compute cap.: 2.0, ECC: yes, stat: compatible #2: NVIDIA Tesla C2070, compute cap.: 2.0, ECC: yes, stat: compatible #3: NVIDIA Tesla C2070, compute cap.: 2.0, ECC: yes, stat: compatible 4 GPUs auto-selected for this run: #0, #1, #2, #3 - - - - Is this a small bug in mdrun? The GPUs are clearly in use even when the message is not displayed. I can see that from the overall performance. I'm using Gromacs 4.6.3 with version 5.0 of the CUDA libraries. Thanks, Jernej -- 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] Potential Energy Scan
Yes. It may be more efficient to group them into a trajectory before calling mdrun. Mark On Aug 2, 2013 7:29 AM, tarak karmakar tarak20...@gmail.com wrote: Thank you Mark. So, if I got it properly, for my system (dihedral scanning), I need to generate configurations, manually, and then perform this 'single point energy calculations' for each of the configurations. If so, then better I would opt for a script to do my job. Regards, Tarak On Thu, Aug 1, 2013 at 5:07 PM, Mark Abraham mark.j.abra...@gmail.com wrote: http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy On Thu, Aug 1, 2013 at 7:03 AM, tarak karmakar tarak20...@gmail.com wrote: Dear All, Can anyone guide me how to perform the 'potential energy scan' for a dihedral of a small molecule in gromacs? Regrads, Tarak -- 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] remd
What does gmxcheck say about them? On Aug 2, 2013 8:08 AM, Shine A shin...@iisertvm.ac.in wrote: Sir, I did an 80 ns Remd simulation, after completion of the simulation extended it up to 480 ns using tpbconv. Now the extended trajectories also write on old trajectory files(traj.trr)? -- 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] Trying to explain differences in behaviour between 2fs and 5fs timesteps
On Fri, Aug 2, 2013 at 4:48 AM, Trayder trayder.tho...@monash.edu wrote: Hi all, I've been running an analysis of the same system (protein/ligand/water/ions) using multiple timesteps (1-5fs) to identify differences in behaviour between the settings. To do this I've compared the energy outputs of the 5 simulations, specifically the averages from g_energy and binning the energies at each step from the log files. What I've found is that 1/2/3fs simulations behave nigh identically, as do 4/5fs. However there is a notable difference between the two groups (graph linked below). I've additionally matched timestep dependent variables between simulations to rule out causes such as different coupling frequencies, the difference was unaffected. The difference in the Total Energy seems to arise from the Coulomb (SR) and LJ-SR terms. While the differences are in the order of 0.1% (~170kJ/mol) I would rest easier being able to explain the sudden change in behaviour from 3-4fs. Anyone have any ideas? Welcome to numerical integration :-) This looks like well-known behaviour (e.g. GROMACS manual 6.7, and refs therein), but it is nice to see it confirmed. Mark Thanks, -Trayder Binned total energies: https://docs.google.com/file/d/0By3TeVcanmk8U0EwXzhNYk5JZUk/edit?usp=sharing 2fs mdp file: integrator = md ; simulation algorithm tinit= 0 dt = 0.002 nsteps = 1000; # steps ; ; Output Control nstxout = 50; write coordinates to .trr nstvout = 50; write velocities to .trr nstlog = 500 ; write energies to .log nstenergy = 500 ; write energies to .edr nstxtcout = 8000 ; write coordinates to .xtc energygrps = Protein OLAT Water_and_Ions ; ; ; Neighbour Searching nstlist = 10 ; update neighbour list ns_type = grid ; neighbour list method pbc = xyz ; periodic boundary conditions rlist = 0.9 ; cut-off for short-range neighbour (nm) cutoff-scheme = verlet ; ; Electrostatics and VdW coulombtype = PME ; type of coulomb interaction rcoulomb= 0.9 ; cut-off distance for coulomb epsilon_r = 1; dielectric constant rvdw= 0.9 ; cut-off for vdw fourierspacing = 0.12 ; maximum grid spacing for FFT pme_order = 4; interpolation order for PME ewald_rtol = 1e-5 ; relative strength of Ewald-shifted DispCorr= EnerPres ; long range dispersion corrections ; ; Temperature Coupling Tcoupl = v-rescale; type of temperature coupling tc-grps = Protein non-Protein ; coupled groups tau_t = .1 .1; T-coupling time constant (ps) ref_t = 310 310 ; reference temperature (K) ; ; Pressure Coupling Pcoupl = parrinello-rahman; type of pressure coupling Pcoupltype = isotropic; pressure coupling geometry tau_p = 2.0 ; p-coupling time constant (ps) compressibility = 4.5e-5 ; compressibiity ref_p = 1.0 ; reference pressure (bar) ; ; Velocity Generation gen_vel = no ; generate initial velocities ; ; Bonds constraints = all-bonds; which bonds to contrain constraint_algorithm= lincs ; algorithm to use lincs_order = 4 lincs_iter = 2 -- View this message in context: http://gromacs.5086.x6.nabble.com/Trying-to-explain-differences-in-behaviour-between-2fs-and-5fs-timesteps-tp5010304.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.
[gmx-users] Re: topology and coordinate file not matching after grompp
oh, sorry. So the error is: Fatal error: Topology include file posre.itp not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors The command I typed: grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr My topol.top: ;GROMACS toplogy ; ;Include the force field #include oplsaa.ff/forcefield.itp ; Include chain topologies #include topol_1AKI.itp #ifdef POSRES #include posre_1AKI.itp #endif #include topol_2CDS.itp #ifdef POSRES #include posre_2CDS.itp #endif ;Include water topology #include spce.itp ;Include generic ion topology #include ions.itp [ system ] Two proteins in water [ molecules ] #mols Protein_1AKI1 Protein_2CDS1 SOL 27020 CL- 16 -- View this message in context: http://gromacs.5086.x6.nabble.com/topology-and-coordinate-file-not-matching-after-grompp-tp5010221p5010309.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
Re: [gmx-users] Re: topology and coordinate file not matching after grompp
On 8/2/13 5:57 AM, chinnu657 wrote: oh, sorry. So the error is: Fatal error: Topology include file posre.itp not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors There are probably #include statements in the .itp files for the proteins, since they were originally .top files written by pdb2gmx. You'll need to get rid of those or otherwise suitably rename them (and then delete the redundant #include statements in the .top). -Justin The command I typed: grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr My topol.top: ;GROMACS toplogy ; ;Include the force field #include oplsaa.ff/forcefield.itp ; Include chain topologies #include topol_1AKI.itp #ifdef POSRES #include posre_1AKI.itp #endif #include topol_2CDS.itp #ifdef POSRES #include posre_2CDS.itp #endif ;Include water topology #include spce.itp ;Include generic ion topology #include ions.itp [ system ] Two proteins in water [ molecules ] #mols Protein_1AKI1 Protein_2CDS1 SOL 27020 CL- 16 -- View this message in context: http://gromacs.5086.x6.nabble.com/topology-and-coordinate-file-not-matching-after-grompp-tp5010221p5010309.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- == 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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Regarding g_order
On 8/2/13 2:04 AM, Venkat Reddy wrote: Thanks Justin for the quick reply. I am simulating a protein with bound lipids. I am in a dilemma to choose the direction of the normal to calculate order parameter. In your *Membrane-protein *simulation tutorial, you have chosen normal to the bilayer along the z-axis. But in my case, there is no bilayer, infact, only few bound lipids are there. In which direction I should choose the normal (*-d option*)? You'll probably have to do some sort of reorienting of the molecules for the results to make sense. -Justin On Thu, Aug 1, 2013 at 10:54 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/1/13 12:07 PM, Venkat Reddy wrote: Dear Gmx-users, In the GROMACS site, it has been mentioned that there is a bug (Instead of numbering carbons from 2-17, the numbering starts from 1-16) in g_order program up to, and including, v4.5.4. But when I am using v4.5.5, I am getting the same sort of numbering. Is it normal or I should renumber from 2-17? If you're getting a number starting with 1, it's probably wrong. You can't calculated Scd for the first carbon in a chain because there is no n-1 carbon from which to determine the necessary vectors. Someone (probably me) updated the wiki when version 4.5.4 was current, so probably any 4.5.x version is really affected, and 4.6.x may be as well, since this really is just a trivial bug that requires simple reinterpretation. -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 -- == 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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Re: topology and coordinate file not matching after grompp
Hi Justin, Yes that was a problem. So after modifying my #include statement in the itp file (initially top. file), it became: ; Include Position restraint file #ifdef POSRES #include posre_2CDS.itp #endif thank you Chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/topology-and-coordinate-file-not-matching-after-grompp-tp5010221p5010312.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] Re: COM of a molecule
If i understand the problem correctly, you can plot the com of any group of atoms as a function of time with g_traj. Create an index file of whatever atoms you want using make_ndx then use g_traj with -com flag to plot com of the group. -- View this message in context: http://gromacs.5086.x6.nabble.com/COM-of-a-molecule-tp5010303p5010313.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
Re: [gmx-users] Using Charmm 36 forcefield on Gromacs 4.6 or higher
On Thu, Aug 1, 2013 at 10:10 PM, akk5r ak...@virginia.edu wrote: Hi All, I am trying to run a membrane protein simulation on Gromacs 4.6 using the Charmm 36 force field parameters. I found the following parameters on the gromacs mailing list for Charmm 36: *; nblist cut-off rlist= 1.2 ; long-range cut-off for switched potentials rlistlong= 1.4 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.2 ; Relative dielectric constant for the medium and the reaction field epsilon_r= 1 epsilon_rf = 1 ; Method for doing Van der Waals vdw-type = switch ; cut-off lengths rvdw-switch = 0.8 rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No * Putting these setting into my .mdp file, I then get this error on grompp: *ERROR 1 [file nvt.mdp]: With Verlet lists only cut-off LJ interactions are supported* I then turned off the Verlet cut-off scheme and was able to create a .tpr file. That's up to you, of course. Your other option is to use Verlet and a plain cut-off at 1.2nm; over the distance from 0.8 and 1.2, the difference between plain cutoff and force-shifted VDW is probably irrelevant anyway. Then I ran my .tpr on mdrun and got the following error: *Program mdrun, VERSION 4.6.1 Source code file: /home/akk5r/Downloads/gromacs-4.6.1/src/kernel/runner.c, line: 824 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors* At this point, I don't know what to do. I have to run this job on a cluster system due to the size of the system. Sure, but your commands to your cluster are setting up the environment with OMP_NUMTHREADS1. With the group scheme, you want one MPI rank per core. Mark Does any one know how to run Charmm 36 simulations on Gromacs 4.6 or higher using Verlet cut-off scheme? Best Wishes, Ali -- View this message in context: http://gromacs.5086.x6.nabble.com/Using-Charmm-36-forcefield-on-Gromacs-4-6-or-higher-tp5010290.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] g_potential and trjconv: problems with bilayer simulation analysis
Hello thanks for the answer I've tried this option, but the obtained result is the g_potential with the popc profile plotted from 0 to 7nm, being one monolayer from 0 to 3.5, region corresponding to water phase at z=3.5 and the other one monolayer from 3.5 to 7. In fact lipid bilayer core is at z=0. The profile present a drift, possibly due to fluctuations in the z (by pressure coupling) and the differences in water density at any side of lipid bilayer. I'm looking in a Gurtovenko's article (J.Chem.Phys 130, 215107 (2009)) a similar artifact regarding time dependence of bilayer electrostatic potential and the drift origin due to bilayer COM fluctuation during simulation. In this paper the authors suggest to center the positions of all the systems atoms with respect to the bilayer COM in each frame. So, is possible to obtain a similar profile, with trjconv tool or any other, but starting at -3.5 to 3.5, with the whole bilayer centered at z=0? Or this result is obtained by mathematic transformation? Thank you 2013/8/1 Justin Lemkul jalem...@vt.edu On 8/1/13 6:55 PM, wood irene wrote: Hi all I'm trying to calculate the electrostatic potential of POPC membrane systems from a trajectory. When I use g_potential, the calculation is well done but the results are plotted from 0 to 7 nm of Z coordinates, with the bilayer center near to 3.5nm. Is possible, modifying the trajectory in order to obtain the results centered in Z=0nm for my membrane simulation? Wich are the steps that I need to follow? I have tried using trjconv but I can not achieve any good solution, with the system centered in bilayer core at z=0. I think that may be using a combination of boxcenter/center, pbc and trans I could resolve it, but I'm not familiar with the correct steps. trjconv -center (centering on POPC) followed by trjconv -trans 0 0 -3.5 -pbc mol should get you pretty close, though if you're using pressure coupling, that 7-nm z-dimension is not fixed so you may need to tweak the translation distance. -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 -- *Ire* -- 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_potential and trjconv: problems with bilayer simulation analysis
On 8/2/13 10:33 AM, wood irene wrote: Hello thanks for the answer I've tried this option, but the obtained result is the g_potential with the popc profile plotted from 0 to 7nm, being one monolayer from 0 to 3.5, region corresponding to water phase at z=3.5 and the other one monolayer from 3.5 to 7. In fact lipid bilayer core is at z=0. The profile present a drift, possibly due to fluctuations in the z (by pressure coupling) and the differences in water density at any side of lipid bilayer. I'm looking in a Gurtovenko's article (J.Chem.Phys 130, 215107 (2009)) a similar artifact regarding time dependence of bilayer electrostatic potential and the drift origin due to bilayer COM fluctuation during simulation. In this paper the authors suggest to center the positions of all the systems atoms with respect to the bilayer COM in each frame. So, is possible to obtain a similar profile, with trjconv tool or any other, but starting at -3.5 to 3.5, with the whole bilayer centered at z=0? Or this result is obtained by mathematic transformation? Gromacs, by default, builds periodic boxes in the positive (x,y,z) dimensions, so no tool will ever report a negative box vector. This is a simple mathematical transformation, or even simpler, just altering the values of the axis, because what you're plotting is exactly what you want. -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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] concatenating 2 xtc files
Sir, But if something went wrong, then over is rather irrelevant, isn't it? Yes. I am planning to rerun ifI dont get any solution. So your simulation started from some previous point and re-ran? I don't see how this would be possible given what you have been posting. The overlap was because. Even though I continued from the ~5ns in 64 cores I had run a little longer in 8 core machine. AS the job was in queue for a long period. That's why I asked before about checking the contents of the .tpr file. You need to verify what it is exactly that you're doing and identify sources of potential problems. Thank you Regards Kavya -- 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] Mean Square Displacement: gromacs 4.5 Vs gromacs 4.6.1
Hi, I performed 2 simulations of a lysozyme in water: one with the version 4.5 of Gromacs and another with the version 4.6.1 (I used the exact same inputs). Then I calculated the MSD and I obtained a complete different behavior with the version 4.6.1 of Gromacs and this MSD is obviously wrong. http://gromacs.5086.x6.nabble.com/file/n5010317/MSD_gmxList.jpg Do you have any ideas what I am doing wrong or did you encounter such a behavior? Regards, Guillaume -- View this message in context: http://gromacs.5086.x6.nabble.com/Mean-Square-Displacement-gromacs-4-5-Vs-gromacs-4-6-1-tp5010317.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
Re: [gmx-users] Mean Square Displacement: gromacs 4.5 Vs gromacs 4.6.1
1ns is rather an eyeblink, and MD is chaotic... what is your evidence that the trend of RMSD either run is representative? Mark On Fri, Aug 2, 2013 at 5:50 PM, Guillaume Chevrot gchev...@cnrs-orleans.fr wrote: Hi, I performed 2 simulations of a lysozyme in water: one with the version 4.5 of Gromacs and another with the version 4.6.1 (I used the exact same inputs). Then I calculated the MSD and I obtained a complete different behavior with the version 4.6.1 of Gromacs and this MSD is obviously wrong. http://gromacs.5086.x6.nabble.com/file/n5010317/MSD_gmxList.jpg Do you have any ideas what I am doing wrong or did you encounter such a behavior? Regards, Guillaume -- View this message in context: http://gromacs.5086.x6.nabble.com/Mean-Square-Displacement-gromacs-4-5-Vs-gromacs-4-6-1-tp5010317.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
[gmx-users] Re: energy conservation / frozen atoms
Thanks for your notes. I did a diagnosis test which could be of relevance here. I set up the following system: [ gas | liquid water (solid water) liquid water | gas ] gas is united atom methane. liquid water is tip4p-ice model and solid water is a cage-like crystalline structure of water and methane called gas hydrate. Now, in order to test the effect of freezing and position restraining on the performance of nve I did two tests at 370 K. Test 1 (freezing): Solid water was kept frozen in all 3 dimensions (Y Y Y). First I ran a nvt for 250 ps for equilibration (potential and total energy both converged after 250 ps, Pressure equilibrated at ~ 3950 bar). Then I started a 1ns nve. Similar to my other simulation, the total energy linearly decreased (0.84% per ns) as well as potential energy. Pressure remained around 3950 bar; however, the temperature decreased from 370 to 364 K (physically, this should not happen). Test 2 (position restraining): Oxygen of solid water was strongly restrained to a point (fc of 10). Similar to the previous test, first I ran a nvt for 250 ps for equilibration (potential and total energy both converged after 250 ps, Pressure equilibrated at about 0 bar with fluctuations of ~ 2000 bar). Then I started a 1ns nve. Again, similar to test 1, the total energy linearly decreased (1.33% per ns) as well as potential energy. Pressure remain around 0 bar; however, the temperature initially dropped from 370 K to 355K within 1 ps, then increased to 358 K during the next 50 ps and thereafter kept linearly decreasing to 353 K until the end of 1 ns run (physically and intuitively, this should not happen). (In both of the tests, I kept the methane inside the cages of solid water position-restrained to a point by fc = 1000). If needed I can post the .mdp and .top files too. I hope this will be helpful from the development standpoint. Regards, Alireza -- Message: 3 Date: Tue, 30 Jul 2013 07:20:53 -0400 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] energy conservation / frozen atoms To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 51f7a195.80...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 7/29/13 10:51 PM, S. Alireza Bagherzadeh wrote: Hi All, I am simulating a system in which I have two solid surfaces and I keep them frozen during simulations. I also exclude the interactions between its atoms to avoid spurious contribution to the virial pressure due to large forces between them as suggested in the manual. I run a nvt for equilibration and then I do the production run in an nve ensemble; however, I am not getting good energy conservation. There is a huge energy drift... When I remove the solid surfaces, I will only have water molecules and united atom methane molecules in my system. Using the same protocol I obtain a very good energy conservation... What happens if you unfreeze the frozen surfaces and run the same system? The point is I do not want to do this as I am trying to save some calculations. My point in asking is to do some diagnostics. There are countless similar posts to yours - freeze some group(s), energy conservation is bad, and then a dead end to the thread. It would be interesting, from a development standpoint, to know whether the issue is truly linked to the frozen group(s). Using strong position restraints in lieu of frozen groups is probably a reasonable workaround that could also be used to find a problem. My system is already big and including all of the bond, angles and dihedral interactions of the solid surfaces slows down the simulation considerably. The bonded interactions are not likely what slows the system down. Freezing doesn't actually improve performance. Using energygrp_excl is what causes a speed-up. Any insight on what might be wrong in my system would be very appreciated. The contents of the .edr file will probably be informative, as you can identify which energy term(s) is(are) most affected. It's all probably related to the frozen surfaces themselves acting as an energy sink or something. Is there anyway to fix the energy sinking effect of the surfaces? That's just an off-the-cuff guess at something being wrong. Like I said above, there's been no thorough evaluation of whether or not this sort of combination does (or should) work. I used dl_poly to simulate a similar system and there was no problem with the energy conservation. That's been reported before, hence something is probably wrong with Gromacs, but we need more information to figure it out and fix it. Otherwise, you'll have to figure out an alternate strategy. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of
Re: [gmx-users] Mean Square Displacement: gromacs 4.5 Vs gromacs 4.6.1
Hi, are you referring to the MSD of the protein? I am not sure which of the MSDs are right, or why there is a difference between the two versions. But, both of the MSDs are plausible. There is no obvious wrong answer. Complex molecules have a long time relaxation and may exhibit glassy behavior and thus an MSD like the blue line. Look at this reference which shows that lipids exhibit sub-diffusive behavior till 30 ns. Protein dynamics are never straightforward. http://pre.aps.org/abstract/PRE/v79/i1/e011907 There is a valid issue about the discrepancy between the two versions. Others may be able to help you here. I suggest longer simulations. On Fri, Aug 2, 2013 at 9:20 PM, Guillaume Chevrot gchev...@cnrs-orleans.frwrote: Hi, I performed 2 simulations of a lysozyme in water: one with the version 4.5 of Gromacs and another with the version 4.6.1 (I used the exact same inputs). Then I calculated the MSD and I obtained a complete different behavior with the version 4.6.1 of Gromacs and this MSD is obviously wrong. http://gromacs.5086.x6.nabble.com/file/n5010317/MSD_gmxList.jpg Do you have any ideas what I am doing wrong or did you encounter such a behavior? Regards, Guillaume -- View this message in context: http://gromacs.5086.x6.nabble.com/Mean-Square-Displacement-gromacs-4-5-Vs-gromacs-4-6-1-tp5010317.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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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: energy conservation / frozen atoms
On 8/2/13 3:19 PM, S. Alireza Bagherzadeh wrote: Thanks for your notes. I did a diagnosis test which could be of relevance here. I set up the following system: [ gas | liquid water (solid water) liquid water | gas ] gas is united atom methane. liquid water is tip4p-ice model and solid water is a cage-like crystalline structure of water and methane called gas hydrate. Now, in order to test the effect of freezing and position restraining on the performance of nve I did two tests at 370 K. Test 1 (freezing): Solid water was kept frozen in all 3 dimensions (Y Y Y). First I ran a nvt for 250 ps for equilibration (potential and total energy both converged after 250 ps, Pressure equilibrated at ~ 3950 bar). Then I started a 1ns nve. Similar to my other simulation, the total energy linearly decreased (0.84% per ns) as well as potential energy. Pressure remained around 3950 bar; however, the temperature decreased from 370 to 364 K (physically, this should not happen). Test 2 (position restraining): Oxygen of solid water was strongly restrained to a point (fc of 10). Similar to the previous test, first I ran a nvt for 250 ps for equilibration (potential and total energy both converged after 250 ps, Pressure equilibrated at about 0 bar with fluctuations of ~ 2000 bar). Then I started a 1ns nve. Again, similar to test 1, the total energy linearly decreased (1.33% per ns) as well as potential energy. Pressure remain around 0 bar; however, the temperature initially dropped from 370 K to 355K within 1 ps, then increased to 358 K during the next 50 ps and thereafter kept linearly decreasing to 353 K until the end of 1 ns run (physically and intuitively, this should not happen). (In both of the tests, I kept the methane inside the cages of solid water position-restrained to a point by fc = 1000). If needed I can post the .mdp and .top files too. An .mdp file would be useful, otherwise a demonstration that these parameters actually produce an energy-conserving NVE ensemble for a simple system. -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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] restraint-lambdas for position restraints in hamiltonian exchange
Hi all, I went through the manual and couldn't find any definite answers to the following questions. First, I wonder if the reference positions of position restraints, not just the force constants, of different replicas are exchanged in hamiltonian exchange based on restraint-lambdas? For example, if I have 1 molecule that has 2 structures, say, A and B and the following 2-component restraint-lambdas: 1.0 1.0 with replica 0 starting in A and replica 1 in B, would the exchange between replica 0 and 1 yield anything meaningful ? In other word, would the relaxation towards the other structure occur in both states once an exchange was accepted? Another question is what types of restraints can restraint-lambdas act on? For example, bond/angle/distance/position restraints, COM-pulling potential ? Thanks, Dejun -- View this message in context: http://gromacs.5086.x6.nabble.com/restraint-lambdas-for-position-restraints-in-hamiltonian-exchange-tp5010322.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
