Re: [gmx-users] Failed to lock: md.log.
You can try move md.log to some folder and then copy back such as: 1) mv md.log /some_folder 2) cp /some_folder/md.log . It works for me Jianguo - Original Message - From: zhaowh zha...@mail.ustc.edu.cn To: gmx-users gmx-users@gromacs.org; gmx-users gmx-users@gromacs.org; gmx-users gmx-users@gromacs.org; gmx-users gmx-users@gromacs.org; gmx-users gmx-users@gromacs.org; gmx-users gmx-users@gromacs.org Cc: Sent: Friday, 14 June 2013, 17:35 Subject: [gmx-users] Failed to lock: md.log. Hi everyone, When I restart the simulation as the following: mdrun -s tpxout -cpi, a fatal error is arised (Fatal error: Failed to lock: md.log. Already running simulation?). But I have the files: md.log, traj.xtc, ender.edr, etc. Thank you for your attention and answer. zhaowh -- 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 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] Performance of Gromacs-4.6.1 on BlueGene/Q
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 1024 1.544 2048 0.978 4092 0.677 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
Re: [gmx-users] Performance of Gromacs-4.6.1 on BlueGene/Q
Thank you, Mark and Xavier. The thing is that the cluster manager set the minimum number of cores of each jobs in Bluegene/Q is 128, so I can not use 64 cores. But according to the performance, 512 cores in Bluegene roughly equivalent to 64 cores in another cluster. Since there are 16 cores in each computational cards, the total number of cores I used in Bluegene//Q is num_cards times 16. So in my test, I acutally run simulations using different number of cards, from 8 to 256. The following is the script I submitted to bluegene using 128 computational cards: #!/bin/sh #SBATCH --nodes=128 # set Use 128 Compute Cards ( 1x Compute Card = 16 cores, 128x16 = 2048 cores ) #SBATCH --job-name=128x16x2 # set Job name #SBATCH -output=first-job-sample # set Output file #SBATCH --partition=training 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 Since bluegene/q accepts up to 4 tasks each core, I used 32 mpi tasks for each card (2 task per core). I tried --ntasks-per-node=64, but the simulations get much slower. Is there a optimized number for --ntasks-per-node? Cheers Jianguo From: Mark Abraham mark.j.abra...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Jianguo Li ljg...@yahoo.com.sg Sent: Tuesday, 4 June 2013, 22:32 Subject: Re: [gmx-users] Performance of Gromacs-4.6.1 on BlueGene/Q On Tue, Jun 4, 2013 at 4:20 PM, XAvier Periole x.peri...@rug.nl wrote: 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. Indeed. Moreover, there is not (yet) any instruction-level parallelism in the GROMACS kernels used on BG/Q, unlike for the x86 family. So there is a theoretical factor of four that is simply not being exploited. (And no, the compiler is not good enough to do it automatically ;-)) Mark 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 1024 1.544 2048 0.978 4092 0.677 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 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 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 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 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] keeping water (entirely) out of the bilayer core
Hi Chris, Just think of another possible way without modifying the code. The task can be achieved by increasing the LJ repulsion term between the lipid tail atoms and water molecules, but keeping all other interactions unchanged. To do so, the free energy code can be used. You can create a state_B, at which only the LJ repulsion term between the lipid tail atoms and water molecules is rescaled, other interactions are the same as state_A, and then run the simulations at lambda=1. Jianguo From: Christopher Neale chris.ne...@mail.utoronto.ca To: gmx-users@gromacs.org gmx-users@gromacs.org Sent: Monday, 6 May 2013, 2:46 Subject: [gmx-users] keeping water (entirely) out of the bilayer core Thank you for the advice Jianguo. This seems like a good way forward. I was hoping not to have to learn how to use new software, but perhaps it is time. Thank you, Chris. -- original message -- Hi Chris, Perhaps you can try PLUMED+GROMACS. In that case, you can define a collective variable as mindist between the water molecules and the lipid tails. And then apply wall potential to keep this CV above a certain value. Jianguo 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. ... -- 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 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] keeping water (entirely) out of the bilayer core
Hi Chris,
Perhaps you can try PLUMED+GROMACS. In that case, you can define a collective
variable as mindist between the water molecules and the lipid tails. And then
apply wall potential to keep this CV above a certain value.
Jianguo
From: Christopher Neale chris.ne...@mail.utoronto.ca
To: gmx-users@gromacs.org gmx-users@gromacs.org
Sent: Saturday, 4 May 2013, 8:46
Subject: [gmx-users] keeping water (entirely) out of the bilayer core
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)
{
int g, 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] fail to pull
You switched on the position restraint in your mdp file, is that the reason? From: Albert mailmd2...@gmail.com To: gromacs maillist gmx-users@gromacs.org Sent: Sunday, 7 April 2013, 2:47 Subject: [gmx-users] fail to pull Dear: I am trying to pull my ligand outside of the binding pocket with following configurations: title = Umbrella pulling simulation define = -DPOSRES ; Pull code pull = umbrella pull_geometry = distance ; simple distance increase pull_dim = Y N N pull_start = yes ; define initial COM distance 0 pull_ngroups = 1 pull_group0 = Protein pull_group1 = LIG pull_rate1 = 0.001 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 Tcoupl = v-rescale tc_grps = Protein_LIG Water_and_ions tau_t = 0.5 0.5 ref_t = 310 310 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 1.0 1.0 compressibility = 4.5e-5 ref_p = 1.0 1.0 refcoord_scaling = com ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr = EnerPres It is quite strange, the ligand is still in place and not outside the pocket at the end of simulations. I am just wondering where is the problem? thank you very much best Albert -- 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 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] Weird result of WHAM
If the two end states of a system are fixed, the free energy difference is independent of the path. I am not sure what caused the problem, but if besides the protein, water and ions, there are some other molecules in your simulation box (e.g., membrane or ligand), the states A and B of your protein from trajectory A-B may not be exactly the same as those from the trajectory B-A. In such a case, it is not strange to have different PMFs. --Jianguo - Original Message - From: Netaly Khazanov neta...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Thursday, 15 November 2012, 15:41 Subject: Re: [gmx-users] Weird result of WHAM Sorry, I will express myself more clearly. 1.State A/B corresponds to different conformation states of the protein. State A is the crystal structure of the protein, suppose to be more stable than state B (model structure). And indeed, I've got the expected PMF plot in which clearly can be seen, that state A is more stable than state B by taking snapshots from the path A to B. In order to check myself, I did the same to the snapshots that were taken from the trajectory path from the B to A and I've got the opposite results. ( State B is more stable than state A by the same magnitude of delta G!) Umbrella sampling for 10ns : ; Pull code pull = umbrella pull_geometry = distance pull_dim = Y Y Y pull_start = yes pull_ngroups = 1 pull_group0 = O1G_O2G_O3G_PG__ATP pull_group1 = r_90 pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 1000 ; kJ mol^-1 nm^-2 pull_nstxout = 1000 ; every 2 ps pull_nstfout = 1000 ; every 2 ps Wham analysis command: g_wham_d -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 1000 2. By merging the data of the both path, I meant that I added tpr files and pullf files from the path B to A to the files tpr-files.dat/ pullf-files.dat of the path A to B and calculated WHAM.. I can do it since it is the same reaction coordinates in both cases, can't I? The result PMF plot shows that state A is more stable than state B like I expected. So I really don't know what I am doing wrong while analysing the snapshots from path B to A. Any ideas? Thanks On Wed, Nov 14, 2012 at 8:40 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/14/12 8:43 AM, Netaly Khazanov wrote: Dear All, I've performed TMD simulation using NAMD program from the state A to B, and visa versa from the state B to A. Umbrella sampling calculations were done on the snapshots that were taken from the path ( A to B B to A) by using Gromacs. Afterwards WHAM analysis was calculated in order to extract PMF plot. However the result of ΔG of PMF plot in the case of A to B path was the opposite (for example -10) than in the case of B to A ( 10). ( I would expect to get the same result in both cases). Can you explain in greater detail what states A and B correspond to? I would expect the opposite - the reverse of a process should have the same magnitude of deltaG and opposite sign (i.e. ligand binding/unbinding). By merging the data of both paths, WHAM gives result of ΔG=-10. The result is very not consistence. I'm probably missing something. You'll have to be more explicit about what you're doing, i.e. actual commands, input, and output. -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 list gmx-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 -- Netaly -- 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 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
Re: [gmx-users] steered pulling code on ligand-receptor complex
If you position restraint the receptor or only use several residues at the binding site, in both cases you limit your sampling to a small part of the phase space and the PMF may not be accurate, since the receptor may undergo conformational change upon ligand binding. Cheers --Jianguo - Original Message - From: 范聪 fanc...@nenu.edu.cn To: gmx-users@gromacs.org Cc: Sent: Tuesday, 30 October 2012, 20:04 Subject: [gmx-users] steered pulling code on ligand-receptor complex Hello, everyone! I'm a new user in gromacs, and now I have to perform a steered pulling code on a ligand-receptor complex. The ligand is to be pulled away from the binding site of the receptor, and umbrella sampling will be used to gain the PMF (potential mean force) curve. Then binding energy of the ligand-receptor complex would be estimated. The receptor contains 303 residues. While the ligand is pulling away, the whole receptor is restrained by posres, 1000 in x, y and z axis. Since the receptor is so large and umbrella sampling needs so much calculations, a very long time will be taken to complete the work. Now I have my question, is there anyway to reduce the taken time? Such as keeping only residues near the binding site to respect the whole receptor? Thank you all in advance! -- 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 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 after TMD of NAMD
It seems difficult to use RMSD as the reaction coordinate to do umbrella sampling simulations. Maybe you can try meta-dynamics in which you can use RMSD as a collective to get the free energy. It is implemented in a modified version of gromacs (GROMETA), or you can use PLUMED together with current Gromacs to do it. -Jianguo From: Netaly Khazanov neta...@gmail.com To: gmx-users@gromacs.org Sent: Wednesday, 17 October 2012, 16:47 Subject: [gmx-users] Umbrella sampling after TMD of NAMD Dear All, I've performed TMD simulation using NAMDprogram. I'd like to calculate PMF plot based on the frames that were taken from TMD simulations by using GROMACS. The coordinate of reaction is RMSD of backbone. The first step is to do Umbrella sampling. The question is how fix the position of backbone during the Umbrella sampling? Is this looks reasonable? pull = umbrella pull_geometry = position ;pull_dim = Y Y Y pull_start = yes pull_ngroups = 1 ;pull_group0 =0 pull_group1 = backbone pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 1000 ; kJ mol^-1 nm^-2 pull_nstxout = 1000 ; every 2 ps pull_nstfout = 1000 ; every 2 ps Any ideas how to convert the reaction coordinate from position of backbone to RMSD of backbone in PMF plot? Thank you in advance. Netaly Khazanov -- Netaly -- 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 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] When are .trr files essential? (was: Regarding Gromacs output files)
One situation is the analysis that require velocities, such as calculating velocity autocorrelation function or lateral pressure. -Jianguo From: Ladasky blind.watchma...@yahoo.com To: gmx-users@gromacs.org Sent: Friday, 12 October 2012, 13:25 Subject: [gmx-users] When are .trr files essential? (was: Regarding Gromacs output files) Erik Marklund wrote On 11 okt 2012, at 16.17, R.Vidya Rajendran (10PHD013) wrote: Hello Friends, I have two very specific queries regarding gromacs output files. 1) Since we can generate .xtc file during mdrun, Is is possible to stop generating .trr files, because it used to be very huge and less useful. Less useful depends on the application, but in many cases yes. Hello Eric, After generating 17 GB of trajectory data, I too am questioning my need for .trr files. Can you take a moment to describe those functions for which .trr files are essential? I can create the PDB files I need to perform visualizations, using trjconv and an .xtc file as input. Macroscopic system parameters are stored in .edr files, and can be extracted using g_energy. If I want to extend a completed run, the .cpt file that was written when the run finished allows me to do that. The only reason that I can see for creating a .trr file is if one might need to start from an EXACT point somewhere in the MIDDLE of a trajectory. What other situations might I be missing? -- View this message in context: http://gromacs.5086.n6.nabble.com/Regarding-Gromacs-output-files-tp5001911p5001929.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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 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] Orientation of protein
editconf -princ will put the long axis of the protein in x-direction, after that you may need editconf -rotate 0 90 0 -c to make it in z-direction -Jianguo - Original Message - From: Shima Arasteh shima_arasteh2...@yahoo.com To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Tuesday, 11 September 2012, 15:18 Subject: [gmx-users] Orientation of protein Hi all, I used this command to put the orientation of protein in z-direction, but didn't work! # editconf -princ -f protein.pdb -o protein-princ.pdb Any suggstions? Is it not the correct command? Sincerely, Shima -- 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 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 (PMF) position discrepancy
I guess is that g_wham takes the distance from tpr file which calculates the distance using grommp. It seems that the distances calculated using g_dist and grompp are different, as discussed in this forum about 10 days ago. -Jianguo - Original Message - From: Raphael Alhadeff raphael.alhad...@mail.huji.ac.il To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Monday, 10 September 2012, 23:54 Subject: Re: [gmx-users] umbrella sampling (PMF) position discrepancy Hi Justin, thank you for you quick reply. On Mon, Sep 10, 2012 at 6:41 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/10/12 11:22 AM, Raphael Alhadeff wrote: Dear Gromacs users, I've been trying to run an umbrella sampling (for the purpose of pmf) using Gromacs 4.5.5. My system consists of a membrane protein transporter and a Na ion passing through it, from the water bulk on one side of the membrane to the water bulk on the other side. I've used the protein as the reference group and the Na ion as the pull group 1 (I've attached the mdp file below). I have used position geometry because to my understanding it is good for the case where the pulled group crosses the reference's COM. I made 31 frames where the ion is 0.2 nm apart, from -2 nm to +2 (in respect to the COM of the protein). I confirmed these distances using g_traj and g_dist on the starting gro files. As I run the g_wham analysis, using -v, I see that the 'position' of each of my frames are highly different than the distances I've measured in the gro files, not only in value but also relative to each other. The same numbers appear in the pull_x or pull_f (after converting appropriately) files. So what I don't understand is how does Gromacs calculate the values for pull_x (and thus for the 'position' for g_wham). I was under the impression it uses COM distance between group0 and group1, but trying to compare using g_traj or g_dist proved me wrong. I have pasted 5 datapoints as an example below, giving the distance measured by g_dist and the distance that pull_x gives: time(ps) g_dist(z) pull_x(1dz) 0 0.894 -1.817 10 0.857 -1.698 20 0.897 -1.866 30 0.890 -1.913 40 0.966 -1.781 50 0.819 -1.76 I've read countless of threads before posting this, and could not find any answer, and will be very appreciative for some light into this. The result of g_dist is the positive root of the distance equation. It also uses x, y, and z components of the distance, while in your case only the z component may be relevant. The dist.xvg file(s) will have each component listed after the total distance in subsequent columns. I understand, and that is what I think I posted in the example. I have the z component of g_dist and following that my umbrella simulation pull_x 1dz value (which according to the parameters I gave in the mdp, should to the best of my knowledge, give the same number) yet the numbers are quite different. I should mention that I am not using positional restraints on the protein. I assume that since the protein is inside the membrane and the ion is much smaller than the protein, the PR is not required, and I wanted the protein to be able to adjust slightly to the movement of the ion (this is a transporter, not a channel). If this is the reason that is causing me trouble I will be happy to have a short explanation on why this makes the distances seem somewhat random. Lastly, I will use this opportunity on the forum to have 2 technical clarifications - -Using pull_init = 0 (or any other number) does not overrun pull_start, rather it adds up, correct? Correct. The output of grompp prints the distances that will be used, as a way to check. -What is the difference between the profile.xvg created (default name) and the pmfintegrated.xvg that is sometimes being created, and how does g_wham decide whether to create one or not? Which flag is giving you pmfintegrated.xvg? That's not a default name, so without your g_wham command line, we can't guess. -Justin That is what I don't understand, I gave no flag for this file, my command line is simply g_wham -ix pull_x.dat -it tpr.dat -v Thank you again, Raphael Thank you very much for the help.. Raphael mdp file: title = pmf integrator = md dt = 0.002 nsteps = 500 ; 10 ns nstcomm = 10 ; Output parameters nstxout = 5000 ; every 10 ps nstvout = 5000 nstxtcout = 5000 ; every 1 ps nstenergy = 5000 ; Bond parameters constraint_algorithm = lincs constraints = all-bonds continuation = yes ; continuing from NPT ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.2 rcoulomb = 1.2 rvdw = 1.2 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.16 pme_order = 4
Re: [gmx-users] Umbrella Sampling Pull code Problem
I have met similar problem before. The distance calculated by g_dist is different from that calculated by grommp, especially when the actual distance between the two groups is very small. As the actual distance becomes larger, the difference of the distance from the two commands becomes smaller. In addition, in my case, when using larger box size, the difference gets smaller. I don't know why, but you may try to use larger box size to minimize the difference. I am also curious of what is the reason. -- Jianguo - Original Message - From: Steinbrecher, Thomas (IPC) thomas.steinbrec...@kit.edu To: gmx-users@gromacs.org gmx-users@gromacs.org Cc: Sent: Friday, 31 August 2012, 19:45 Subject: [gmx-users] Umbrella Sampling Pull code Problem Dear Gromacs users, I have encountered a strange problem when trying to set up umbrella sampling simulations using gromacs 4.5.3. My system contains two groups with a COM distance of 1.95 nm (all distances measured by g_dist). Trying to set up the first US window, I use the following pull code, together with typical mdp parameters from the Gromacs US tutorial: ; pull options pull = umbrella pull_geometry = distance pull_dim = Y Y Y pull_start = yes pull_init1 = 0.00 pull_nstxout = 1 pull_nstfout = 0 pull_group0 = Protein pull_group1 = OHM pull_rate1 = 0.0 pull_k1 = 1 this results in a simulation in which the group distance remains close to 1.95nm, as expected. However, when I make the following two changes in my input file: pull_start = no pull_init1 = 1.95 which should (?) amount to an equivalent setup, a very different trajectory results in which the COM distance quickly increases to 2.7 nm and then appears to be restrained there. (Visualization confirms, in the first case, the groups remain in their starting conformation, in the second one, they are pushed appart) Interestingly, the grompp output contains the following lines: Pull group natoms pbc atom distance at start reference at t=0 0 994 497 1 2 46347 1.224 1.950 in this case. Apparently, grompp (and mdrun thereafter) calculates the group COM distance differently from g_dist! I think this is not a PBC issue, every atomic distance within both groups is smaller than half the box size and the pbcatoms are close together. However, when I set pbcatom0 to various atom numbers, different 'distance at start' values are obtained, but never the correct COM distance. The two groups do not have overlapping atoms. I am sure I used the same group indexes for pulling and distance measurements. This behaviour is so visibly wrong that I cannot believe this is a bug and rather think I am doing something incorrect. A search of the list revealed a somewhat similar report by Gavin Melaugh in 2011 which did not resolve the issue. Any ideas on what might be the problem here? I am willing to send around files to reproduce the problem of course. Thomas Dr. Thomas Steinbrecher Institut für Physikalische Chemie, KIT Kaiserstr. 12, 76131 Karlsruhe-- 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 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] Protein-POPC bilayer
After inserting the protein, the equilibrium box length in the x and y dimension should be different, so you need anisotropic pressure coupling during the 1st step. After equilibrium, the ratio of box length in x,y is fixed, so you can use semi-isotropic method. --Jianguo From: Shima Arasteh shima_arasteh2...@yahoo.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, 17 August 2012, 7:26 Subject: [gmx-users] Protein-POPC bilayer Hi, I have a question about the Protein-POPC system: To insert a protein in lipid bilayer, I am suggested to simulate POPC in water separately before insertion, it might decrease the time of final simulation. It's OK! In the article suggested me by dear Peter C. Lai, I read that POPC was simulated in anisotropic pressure coupling at first and then after insertion of protein, semi-isotropic pressure coupling is applied. Now, would you please telling me why you used this procedure? And, Would my system be correct if I use semi-isotropic pressure coupling instead of anisotropic pressure coupling for the first step? Thanks in advance for your replies. Sincerely, Shima -- gmx-users mailing list gmx-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] Protein-POPC bilayer
What I think is that anisotropic coupling may be faster in equilibrium. Suppose the protein is quite different in x and y dimensions, after insertion, I think it is faster to get equilibrium the box length separately. I agree with you that semi-isotropic coupling in the first step can also do the job, but I expect it may take longer time to reach equilibrium. --Jianguo From: Justin Lemkul jalem...@vt.edu To: Jianguo Li ljg...@yahoo.com.sg; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, 17 August 2012, 9:19 Subject: Re: [gmx-users] Protein-POPC bilayer On 8/16/12 9:14 PM, Jianguo Li wrote: After inserting the protein, the equilibrium box length in the x and y dimension should be different, so you need anisotropic pressure coupling during the 1st step. After equilibrium, the ratio of box length in x,y is fixed, so you can use semi-isotropic method. Most pre-equilibrated bilayers have (roughly) equivalent x and y box dimensions. Why do you think they should inherently be different? In my experience, anisotropic coupling leads to major deformations in the x-y plane, taking a bilayer that is initially a square (roughly) in the x-y plane and turning it into a rectangle. I'd be very curious to hear Peter's answer to this question. I used to use anisotropic coupling, but now I use semiisotropic exclusively. -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 * 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] how to build a mixed lipid bilayer?
There are several ways, usually I do like the following: 1. first construct one leaflet. Use editconf -translate to construct a small box containing with 3 POPE 1 POPE 2. Use genconf -nbox to replicate the above in x,y dimension to get 64 lipids 3. Use editconf -rotate -translate to get the another leaflet with 64 lipids 4. Use cat to conbine the two leaflet 5. Use grep and cat commands to re-order the lipids. 6. Change the z dimension of the box. Also change vdwradii.dat and solvate the system and add counter ions. After that run a long simulation to equilibrate the system. btw, which force field you want? If you use gromos force field, you can download the itp and pdb files from http://www.softsimu.net/downloads.shtml If you want CHARMM36, I can send you the files. -Jianguo From: xi zhao zhaoxiitc2...@yahoo.com.cn To: gmx-users@gromacs.org Sent: Sunday, 29 July 2012, 9:19 Subject: [gmx-users] how to build a mixed lipid bilayer? Dear Users: I would like to build a mixed lipid bilayer (POPE/POPG=3:1) in the MD using Gromacs, please provide some tools for producing the structures or existing structures (PDB or gro files). Thank you very much! -- gmx-users mailing list gmx-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] cutting a cylinder from simulation box
Maybe you can try trjorder to order the water molecules around your protein and make a group of those nearest water molecules and output them using trjconv Jianguo From: Sanku M msank...@yahoo.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, 28 February 2012, 7:49 Subject: [gmx-users] cutting a cylinder from simulation box Hi, I have run a simulation of a fixed object in water using gromacs. Now, I want to analyze only water molecules which are present within a cylinder of certain radius (smaller than simulation box dimension in XY plane). I wonder whether gromacs has any particular tool which can identify the particles within a cylindrical volume of a simulation box. Thanks Sanku -- 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 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] Free energy between surfaces
One way to get the free energy is to measure the force as a function of distance and do the integration to get the PMF, as used in the paper: Ronen Zangi, Morten Hagen, and B. J. Berne. 2007. Effect of Ions on the Hydrophobic Interaction betweenTwo Plates. J. AM. CHEM. SOC. 2007, 129, 4678-4686 Jianguo From: Steven Neumann s.neuman...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, 18 February 2012, 17:25 Subject: [gmx-users] Free energy between surfaces Dear Gmx Users, I am wondering whether you know a technique for calculating the free energy between charged surfaces - I want to calculate distance when the deltaG=0 so that the surfaces are in equilibrium - closer distance will make that they repeal each other, longer (deltaG0). Will Umbrella Samling would be ok for those calculations? If I pull a whole surface away from another (in NPT) the box vectors will descrease to maintain the same density of water. Thus, the surface will be smaller, am I right? How about pbc? If you have any ideas, please share! Steven -- 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 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] Water Shell Density
Probably you can use g_rdf -surf to get the surface based g(r) for water molecules, since g(r) is the local_density divided by the average_density, then local_density=g(r)_surf*average_density, which is a function of distance from the surface. Jianguo From: Yao Yao ya...@ymail.com To: gmx-users@gromacs.org gmx-users@gromacs.org Sent: Thursday, 16 February 2012, 3:01 Subject: [gmx-users] Water Shell Density Hi Gmxers, Is there a way to calculate the density of water in a protein hydration layer, like from 5 A to 10 A (radius) from the protein surface? Thanks, Yao -- 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 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 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 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] the ligang topology
This paper has used united atoms for -CF3 and -CF2: Hiroaki et al. Enhanced Hydrophobicity of Fluorinated Lipid Bilayer: A Molecular Dynamics Study. J. Phys. Chem. B 2008, 112, 11305–11309. Another way is to use ATB to generate the topology, but I am not sure if it can deal with fluorine atom. http://compbio.biosci.uq.edu.au/atb/ Jianguo From: xiaojiong xiaoji...@zju.edu.cn To: gmx-users@gromacs.org Sent: Wednesday, 15 February 2012, 19:35 Subject: [gmx-users] the ligang topology Dear, The topology for my ligand was created employing the server PRODRG 2.5 Beta. Now I change the charges to consistent with the GROMOS96,but I don't know the charges of -CF3 and C-Cl .Where can I find or can you tell me?Thanks! -- 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 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] water channel
You can look at gromacs tool g_flux and g_count at: https://github.com/orbeckst/g_count Jianguo From: Yao Yao ya...@ymail.com To: gmx-users@gromacs.org gmx-users@gromacs.org Sent: Wednesday, 15 February 2012, 10:38 Subject: [gmx-users] water channel Hi Gmxers, Happy Valentine's Day! Sorry, I am still simulating a protein that has water channel. I was just wondering if there is a way to calculate the water density in the channel throughout my trajectory. I was lucky enough to run a NPT simulation. So I guess I can use g_energy to directly get density. But since the number of the channel water is quite dynamic, I do not think I can separate energy group for them in my mdp. Could someone help me with this? Thanks, Yao -- 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 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] Orders of the residues in gromacs
Another possible reason is due to vmd, which numbers the residue from 0. Residue 143 in gromacs corresponds to residue 142 in vmd. Cheers, Jianguo From: Du Jiangfeng (BIOCH) j...@maastrichtuniversity.nl To: gmx-users@gromacs.org gmx-users@gromacs.org Sent: Friday, 3 February 2012, 1:16 Subject: [gmx-users] Orders of the residues in gromacs Dear Friends, I want to measure some data of a special residue, for instance TRP143, from my MD result. But i encountered a problem. The residue number 143 is ordered in .gro file, while it seems the residue orders is random in gromacs. It points to another residue when I specify residue number 143 in VMD or when I am using make_ndx program ( -- r 143; q). Apparently, gromacs numbering system is not based on the orders in the .gro structure file. Does anybody know how to link the gromacs order to the structure file's order correctly? Thank you in advance, Jiangfeng. Jiangfeng Du, PhD Student Cardiovascular Research Institute Maastricht Department of Biochemistry P.O. Box 616 Mobile: +31-681741859 FAX: +31-43-3884159 6200 MD Maastricht The Netherlands-- 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 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] Failed to lock: md.log. No locks available.
There is a solution in this mailing list sometime before: mv md.log to some other folder and copy it back. Jianguo From: lina lina.lastn...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, 13 January 2012, 18:51 Subject: Re: [gmx-users] Failed to lock: md.log. No locks available. On Fri, Jan 13, 2012 at 4:57 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 13/01/2012 7:08 PM, lina wrote: Hi, Failed to lock: md.log. No locks available. mdrun locks various files at various points. If it can't then GROMACS won't continue, but the problem lies with the file system, and not with GROMACS. Possibly some phantom process still thinks it owns the file. It's something relevant to the server. I am not experienced to figure it out even did some rough try. will drop an email to administrator. Thanks, Mark still the same problem I met before, once I terminated, resume not work, there is a md.log file. $ mount /dev/sda1 on / type ext3 (rw) none on /proc type proc (rw) none on /sys type sysfs (rw) none on /dev/pts type devpts (rw,gid=5,mode=620) usbfs on /proc/bus/usb type usbfs (rw) none on /dev/shm type tmpfs (rw) none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw) sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw) honeydewlocal:/vol/hpc_vol/HomeHPC on /home type nfs (rw,rsize=32k,wsize=32k,intr,hard,tcp,addr=192.168.5.83) The /home is mounting on the last one. CPU: 8 Intel(R) Xeon(R) Dual-Core 3.33 Ghz Memory: 114GB RAM HDD Size: 744GB OS: CentOS 4 (64-bits) Thanks for any suggestions, any additional info you need please let me know, Best regards, -- 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 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 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 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] CMAP for alanine dipeptide in Charmm27 ff
which gromacs version are you using? cMAP is implemented in v4.5 or later Jianguo From: César Ávila clav...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, 9 October 2011 12:07 AM Subject: [gmx-users] CMAP for alanine dipeptide in Charmm27 ff I would like to run REMD simulations on the alanine dipeptide using the Charmm27ff + CMAP. Still, after processing the pdb with pdb2gmx, I do not see any entrance referring to the cmap term in the topology file. Does this mean that Cmap won't be calculated? -- 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 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] CMAP for alanine dipeptide in Charmm27 ff
After checking the topology of my peptide, I found that every term in the cMAP section involve three consecutive residues. So I guess no cMAP term is required for di-ALA. Jianguo --- On Mon, 10/10/11, César Ávila clav...@gmail.com wrote: From: César Ávila clav...@gmail.com Subject: Re: [gmx-users] CMAP for alanine dipeptide in Charmm27 ff To: Jianguo Li ljg...@yahoo.com.sg, Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, 10 October, 2011, 5:51 PM v4.5.4 As I commented above, I had to manually add an entrance for the cmap terms in the topology file as pdb2gmx would not generate them for the alanine dipeptide. There seems to be no problem for larger peptides. Cheers Cesar 2011/10/10 Jianguo Li ljg...@yahoo.com.sg which gromacs version are you using? cMAP is implemented in v4.5 or later Jianguo From: César Ávila clav...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, 9 October 2011 12:07 AM Subject: [gmx-users] CMAP for alanine dipeptide in Charmm27 ff I would like to run REMD simulations on the alanine dipeptide using the Charmm27ff + CMAP. Still, after processing the pdb with pdb2gmx, I do not see any entrance referring to the cmap term in the topology file. Does this mean that Cmap won't be calculated? -- 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 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 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 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: about non-writing issue
I met the similar problem before, sometimes my job writes output, sometimes not. My cluster administrator fixed the problem and they told me that there were some problem at some compute nodes which my job unfortunately was dispatched to. Jianguo From: lina lina.lastn...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, 18 September 2011 5:13 PM Subject: [gmx-users] Re: about non-writing issue Hi, It works now. Not write (just based on guess) might the md.log step such as is 1114 while use thread I noticed the actually run step started from 11135000 so I run until it can write to the md.log then switch to 1 node to run for a while, then switch to more nodes. But there might be some reason there which I don't know. Thanks, On Sun, Sep 18, 2011 at 4:35 PM, lina lina.lastn...@gmail.com wrote: Hi, Very sporadically and also with high frequent, The job I submitted only running without writing (this job is not un-started one, mainly one I stopped and rerun). Before I thought I did not wait long enough, such as hours, but seriously after 3 or 8 hours, still running not writing. I ssh to each nodes, all is fully running. The storage is NFS, I/O flow can't be choked for hours. Really headache, sometimes it works. I have had no clue about it. Thanks for any suggestions, -- Best Regards, lina -- Best Regards, lina -- 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 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] residue numbering different
The first residue number in VMD is 0, not 1. Jianguo From: aiswarya pawar aiswarya.pa...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, 16 September 2011 1:21 PM Subject: [gmx-users] residue numbering different Hi Users, When i list the residues in a index file it shows a numbering of residues and when open the same protein in VMD and check the residue numbering its different. i want to visualise the protein in VMD and select a residue number from VMD and use in gromacs ie want to make an index file in gromacs so how would go about. Thanks -- 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 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] how to handle different atom names between pdb and rtp files.
You can either use -ighn option in pdb2gmx or mannualy rename the atom names in the pdb file. Cheers, Jianguo From: KONG Xian xiansh...@gmail.com To: gmx-users@gromacs.org Sent: Tuesday, 13 September 2011 15:36:41 Subject: [gmx-users] how to handle different atom names between pdb and rtp files. Hello, I’ve got a pdb file,but while I convert it to gro files, I met such problem: Atom HA in residue MET 1 was not found in rtp entry MET with 11 atoms while sorting atoms I find that in the rtp files of the ff files, the H atom linked with C-alpha is called H, but in the pdb file, the same hydrogen atom is called HA, I think this may be the problem. So, my problem is, how to convert my pdb files to make the atom names consistent between the pdb and rtp files? KONG Xian Tsinghua University, Beijing, China 2011/9/13 __ Information from ESET NOD32 Antivirus, version of virus signature database 6458 (20110912) __ The message was checked by ESET NOD32 Antivirus. http://www.eset.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] Error when performing grompp on lipid bilayer modeled with CHARMM27
Why not use CHARMM36 FF? It is available in gromacs user contribution website. If I remember correctly, charmm27 cannot yield correct area/lipid, you need to apply surface tension. Cheeers, Jianguo From: Jackson Chief jchief...@gmail.com To: gmx-users@gromacs.org Sent: Monday, 5 September 2011 21:20:48 Subject: [gmx-users] Error when performing grompp on lipid bilayer modeled with CHARMM27 I want to make a model of a GPCR inserted into lipid bilayer. I obtained the structure file for a solvated POPC bilayer from the CHARMM-GUI site. I used CHARMM27 force field to model the bilayer and pdb2gmx had no problem generating the *.gro, *.top, and posre.itp files. When I perform grompp I receive the following warning and error; WARNING 1 [file ffnonbonded.itp, line 130]: Overriding atomtype HOL ERROR 1 [file bilayer.top, line 271489]: No default U-B types I though that the issue with creating Urey-Bradley interactions using pdb2gmx had been corrected in Gromacs-4.5.4. Please give me some advice on how to proceed further. Thank you, Jackson Chief Elk-- 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:You might need to add atom H to the hydrogen database of residue
you may need to use -ignh option in pdb2gmx. Jianguo From: Kamesh Narasimhan g0701...@nus.edu.sg To: gmx-users@gromacs.org gmx-users@gromacs.org Sent: Wednesday, 24 August 2011 14:42:28 Subject: [gmx-users] error:You might need to add atom H to the hydrogen database of residue Hi all, I am using Gromacs 4.0.5 with the forcefield amber03 in a red hat linux machine to simulate a protein-DNA complex. Eventhough I manually edited my pdb file to adhere to the amber nomenclature, I get the below error. I have not been able to pinpoint where in the pdb file, ffamber03.rtp, and ffamber03.hdb the error could be -- if it's a nomenclature error. Would be great to receive some pointers on this. pdb2gmx -f prim_amb.pdb -o prim_amb.gro -water spc -ff amber03 . . . . . WARNING: atom H is missing in residue GLY 1 in the pdb file You might need to add atom H to the hydrogen database of residue GLY in the file ff???.hdb (see the manual) - Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2top.C, line: 704 Fatal error: There were 1 missing atoms in molecule Protein_C, if you want to use this incomplete topology anyhow, use the option-missing. I get the error message complaining about a missing hydrogen in the first residue, no matter what that residue is --- say for instance even if I delete the first GLY residue from my pdb file. krish-- 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:You might need to add atom H to the hydrogen database of residue
Not sure what is the problem. but if you have changed the name of the first/last residue as NXXX/CXXX, you may try to add these two names (NXXX and CXXX) to aminoacids.dat file (also change the number in the first line). Cheers, Jianguo From: Kamesh Narasimhan g0701...@nus.edu.sg To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, 24 August 2011 15:10:13 Subject: RE: [gmx-users] error:You might need to add atom H to the hydrogen database of residue Thanks Jianguo, It doesn't seem to make a difference even if i use -ignh -- I still get the same error. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Jianguo Li [ljg...@yahoo.com.sg] Sent: Wednesday, August 24, 2011 3:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] error:You might need to add atom H to the hydrogen database of residue you may need to use -ignh option in pdb2gmx. Jianguo From: Kamesh Narasimhan g0701...@nus.edu.sg To: gmx-users@gromacs.org gmx-users@gromacs.org Sent: Wednesday, 24 August 2011 14:42:28 Subject: [gmx-users] error:You might need to add atom H to the hydrogen database of residue Hi all, I am using Gromacs 4.0.5 with the forcefield amber03 in a red hat linux machine to simulate a protein-DNA complex. Eventhough I manually edited my pdb file to adhere to the amber nomenclature, I get the below error. I have not been able to pinpoint where in the pdb file, ffamber03.rtp, and ffamber03.hdb the error could be -- if it's a nomenclature error. Would be great to receive some pointers on this. pdb2gmx -f prim_amb.pdb -o prim_amb.gro -water spc -ff amber03 . . . . . WARNING: atom H is missing in residue GLY 1 in the pdb file You might need to add atom H to the hydrogen database of residue GLY in the file ff???.hdb (see the manual) - Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2top.C, line: 704 Fatal error: There were 1 missing atoms in molecule Protein_C, if you want to use this incomplete topology anyhow, use the option-missing. I get the error message complaining about a missing hydrogen in the first residue, no matter what that residue is --- say for instance even if I delete the first GLY residue from my pdb file. krish-- 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] Convert drug Charmm topology to Gromacs
Hi, The .str file contains the information of atomtype, bonds and improper dihedrals, so it is eneough to write a .rtp file. Then using pdb2gmx to generate the itp file. And you also need to add the missing parameters from CgenFF into the itp parameter files based on chapter 5, as Justin suggested. best regards, Jianguo From: Steven Neumann s.neuman...@gmail.com To: gmx-users@gromacs.org Sent: Wednesday, 24 August 2011 20:26:13 Subject: [gmx-users] Convert drug Charmm topology to Gromacs Dear Gromacs Users, I have generated topology file for CHARMM ff using online server for my small molecule (I obtained .str file). How can I convert it into the Gromacs topology file (.itp)? Thanks, Steve -- 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] the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure
Hi, Kong Xian, It is better to use SHAKE instead of LINCS since LINCS does not directly yield pairwise forces, as shown in the paper: Erik Lindahl and Olle Edholm. Spatial and energetic-entropic decomposition of surface tension in lipid bilayers from molecular dynamics simulations. JOURNAL OF CHEMICAL PHYSICS, VOLUME 113, NUMBER 9, 3882–3893. best regards, Jianguo From: KONG Xian xiansh...@gmail.com To: gmx-users@gromacs.org Sent: Friday, 19 August 2011 23:50:01 Subject: [gmx-users] the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure I have sent this email days ago, but I got no answer. Hope someone would saw it this time. Sorry for disturbing. Dear all: I am using gromacs-4.0.2_localpressure to calculate the local pressure of my system. I have a question. When rerun the mdrun from gromacs-4.0.2_localpressure I used a new .mdp file. There are some changes of the new .mdp file according the original one. I have 2 questions: 1. I changed the The coulomb interaction type from PME to reaction field with epsilon_r=1 epsilon_rf=78; Is this change feasible? 2. I used LINCS for all bonds in the simulation, and I still use the LINCS for all bonds when calculate the local pressure. Is this way right? Thanks for any reply. Best wishes, KONG Xian Tsinghua, Beijing, China __ Information from ESET NOD32 Antivirus, version of virus signature database 6393 (20110819) __ The message was checked by ESET NOD32 Antivirus. http://www.eset.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: Re：the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure
From: KONG Xian xiansh...@gmail.com To: ljg...@yahoo.com.sg Cc: gmx-users@gromacs.org Sent: Sunday, 21 August 2011 19:20:50 Subject: Re：the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure Thanks for your kindly reply. I used the LINCS calculated the pressure field. The distinct between protein and the lipid bilayer is obvious from the pressure field. But the lipid bilayer and the water is not very obvious , they seems to be a uniform from the pressure field calculated. As in Ollila’s original paper: 3D Pressure Field in Lipid Membranes and Membrane-Protein Complexes, there is an distinct separation region between membrane and the water. Maybe the LINCS is the problem. Another problem is perhaps the localpressure software is for CG model? My model is all-atom model and the simulation time length is not long enough, maybe this is the cause of the results? -- From my limited experience, the local pressure calculation converges very poorly. It takes more than 50 ns of production run in my case to get a converged profile. You can divide the production run into several sub-trajectories to judge the convergence. KONG Xian 2011/8/21 Hi, Kong Xian, It is better to use SHAKE instead of LINCS since LINCS does not directly yield pairwise forces, as shown in the paper: Erik Lindahl and Olle Edholm. Spatial and energetic-entropic decomposition of surface tension in lipid bilayers from molecular dynamics simulations. JOURNAL OF CHEMICAL PHYSICS, VOLUME 113, NUMBER 9, 3882b3893. best regards, Jianguo From: KONG Xian xiansh...@gmail.com To: gmx-users@gromacs.org Sent: Friday, 19 August 2011 23:50:01 Subject: [gmx-users] the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure I have sent this email days ago, but I got no answer. Hope someone would saw it this time. Sorry for disturbing. Dear all: I am using gromacs-4.0.2_localpressure to calculate the local pressure of my system. I have a question. When rerun the mdrun from gromacs-4.0.2_localpressure I used a new .mdp file. There are some changes of the new .mdp file according the original one. I have 2 questions: 1. I changed the The coulomb interaction type from PME to reaction field with epsilon_r=1 epsilon_rf=78; Is this change feasible? 2. I used LINCS for all bonds in the simulation, and I still use the LINCS for all bonds when calculate the local pressure. Is this way right? Thanks for any reply. Best wishes, KONG Xian Tsinghua, Beijing, China __ Information from ESET NOD32 Antivirus, version of virus signature database 6397 (20110821) __ The message was checked by ESET NOD32 Antivirus. http://www.eset.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: local pressure v4.5 issues
Use grompp of v4.0.7 to generate the tpr files using CHARMM FF and give this tpr file to v4.0.2_local_pressure to rerun the simulation. Jianguo From: Amit Choubey kgp.a...@gmail.com To: Jianguo Li ljg...@yahoo.com.sg Cc: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, 28 July 2011 09:27:04 Subject: Re: [gmx-users] Re: local pressure v4.5 issues Hi all, I am trying to figure out a way to port tpr files (which has CHARMM FF) from v4.5 to v4.0.2. This is because i want to use the localpressure calculation which works only in version 4.0.2. When i issue the following command i get grompp_v4.0.2_lp -v -c traj0.gro -o npt_4.0 -p system.top -f rerun.mdp I get the following error Program grompp_v4.0.2_lp, VERSION 4.0.2_localpressure Source code file: topdirs.c, line: 118 Fatal error: Invalid dihedral type 9 I think dihedral type 9 is not defined until version 4.0.7. Could anyone provide a way to deal with this ? Amit On Thu, Jun 30, 2011 at 9:39 PM, Jianguo Li ljg...@yahoo.com.sg wrote: I downloaded v4.5 and v4.0 from the same websites as you mentioned in previous email. I am not sure why v4.5 give inconsistent results. I haven't try v4.0, because my simulation is using CHARMM FF. Could you give more details of conversion tpr files from v4.5 to v4.0 using CHARMM FF? Thank you very much! Cheers, Jianguo From: Amit Choubey kgp.a...@gmail.com To: Jianguo Li ljg...@yahoo.com.sg Cc: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, 1 July 2011 11:47:58 Subject: Re: [gmx-users] Re: local pressure v4.5 issues On Thu, Jun 30, 2011 at 7:57 PM, Jianguo Li ljg...@yahoo.com.sg wrote: Hi Amit, I also encountered the same problem you mentioned. In v4.5, when using -nstlp wiht large value (e.g., 1000), I got one file localpressure.dat0. I tested first several frames of a trajectory, the calculated pressure is not the average of the pressure of individual frames. In v4.5 it outputs the profile for frames in separate files which is ok. My concern is what exactly is going in v 4.0 where there is only one file for all the frames. Also where did you download v4.5 and v4.0 from ? Btw, did you use CHARMM FF in your simulations and how did you convert the tpr files from v 4.5 to v 4.0? Yes i have used CHARMM FF and i will have to figure out the conversion. Cheers Jianguo From: Amit Choubey kgp.a...@gmail.com To: Jianguo Li ljg...@yahoo.com.sg; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, 1 July 2011 10:32:07 Subject: Re: [gmx-users] Re: local pressure v4.5 issues Hello Everyone, The git version of local pressure calculation at http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure is broken. I could not get it to work for my simulations. I installed gromacs local pressure version 4.0 from ftp://ftp.gromacs.org/pub/tmp/ I used gromacs-4.0.2_localpressure.tar.gz in that folder. The pressure values printed using this version seem reasonable to me. I converted all the tpr files from v 4.5 to v 4.0. The output of the mdrun in v 4.0 is a single file localpressure.dat . On the contrary in v 4.5 there were separate localpressure.dat* files for each frame. I am not sure what exactly is the content of localpressure.dat. Does it have the time averaged value of pressure tensor for each voxel ? It doesnt seem so to me because i tried it over only two frames (3 reruns were done for two frames separately and a .trr which had these two frames only) and the numbers did not seem to be averages. Can someone help me in figuring out what is going on ? Amit On Tue, Jun 21, 2011 at 9:16 AM, Amit Choubey kgp.a...@gmail.com wrote: On Tue, Jun 21, 2011 at 1:13 AM, Jianguo Li ljg...@yahoo.com.sg wrote: Hi Amit, May I ask you a question? In your calculation of local pressure using a trajectory file, did you get a single averaged localpressure.dat file? Or else you get a bunch of separate files for each frame (e.g., localpressure.dat0, localpressure.dat1, localpressure.dat2 )? Yes I do get different files for different trajectories. All the files seem to have the same problem ie a very large/small number printed as tensor elements of the pressure for some of the voxels. Do you have such problems ? Could we compare our methodologies to use the local pressure version ? Amit Thank you very much! Cheers, Jianguo From: Amit Choubey kgp.a...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, 20 June 2011 07:08:03 Subject: [gmx-users] Re: local pressure v4.5 issues Dear all, I did another simulation with only SPC water. Then I used the local pressure gromacs to calculate the stresses. It seems to be reasonable. I am not sure how to figure out what goes wrong with my
Re: [gmx-users] Re: local pressure v4.5 issues
I have tried CHARMM FF in v4.0.4 and it does not give error, so it seems dihedral type 9 has already been implemented in v4.0.4. Jianguo From: Jianguo Li ljg...@yahoo.com.sg To: Amit Choubey kgp.a...@gmail.com Cc: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, 28 July 2011 15:05:19 Subject: Re: [gmx-users] Re: local pressure v4.5 issues Use grompp of v4.0.7 to generate the tpr files using CHARMM FF and give this tpr file to v4.0.2_local_pressure to rerun the simulation. Jianguo From: Amit Choubey kgp.a...@gmail.com To: Jianguo Li ljg...@yahoo.com.sg Cc: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, 28 July 2011 09:27:04 Subject: Re: [gmx-users] Re: local pressure v4.5 issues Hi all, I am trying to figure out a way to port tpr files (which has CHARMM FF) from v4.5 to v4.0.2. This is because i want to use the localpressure calculation which works only in version 4.0.2. When i issue the following command i get grompp_v4.0.2_lp -v -c traj0.gro -o npt_4.0 -p system.top -f rerun.mdp I get the following error Program grompp_v4.0.2_lp, VERSION 4.0.2_localpressure Source code file: topdirs.c, line: 118 Fatal error: Invalid dihedral type 9 I think dihedral type 9 is not defined until version 4.0.7. Could anyone provide a way to deal with this ? Amit On Thu, Jun 30, 2011 at 9:39 PM, Jianguo Li ljg...@yahoo.com.sg wrote: I downloaded v4.5 and v4.0 from the same websites as you mentioned in previous email. I am not sure why v4.5 give inconsistent results. I haven't try v4.0, because my simulation is using CHARMM FF. Could you give more details of conversion tpr files from v4.5 to v4.0 using CHARMM FF? Thank you very much! Cheers, Jianguo From: Amit Choubey kgp.a...@gmail.com To: Jianguo Li ljg...@yahoo.com.sg Cc: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, 1 July 2011 11:47:58 Subject: Re: [gmx-users] Re: local pressure v4.5 issues On Thu, Jun 30, 2011 at 7:57 PM, Jianguo Li ljg...@yahoo.com.sg wrote: Hi Amit, I also encountered the same problem you mentioned. In v4.5, when using -nstlp wiht large value (e.g., 1000), I got one file localpressure.dat0. I tested first several frames of a trajectory, the calculated pressure is not the average of the pressure of individual frames. In v4.5 it outputs the profile for frames in separate files which is ok. My concern is what exactly is going in v 4.0 where there is only one file for all the frames. Also where did you download v4.5 and v4.0 from ? Btw, did you use CHARMM FF in your simulations and how did you convert the tpr files from v 4.5 to v 4.0? Yes i have used CHARMM FF and i will have to figure out the conversion. Cheers Jianguo From: Amit Choubey kgp.a...@gmail.com To: Jianguo Li ljg...@yahoo.com.sg; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, 1 July 2011 10:32:07 Subject: Re: [gmx-users] Re: local pressure v4.5 issues Hello Everyone, The git version of local pressure calculation at http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure is broken. I could not get it to work for my simulations. I installed gromacs local pressure version 4.0 from ftp://ftp.gromacs.org/pub/tmp/ I used gromacs-4.0.2_localpressure.tar.gz in that folder. The pressure values printed using this version seem reasonable to me. I converted all the tpr files from v 4.5 to v 4.0. The output of the mdrun in v 4.0 is a single file localpressure.dat . On the contrary in v 4.5 there were separate localpressure.dat* files for each frame. I am not sure what exactly is the content of localpressure.dat. Does it have the time averaged value of pressure tensor for each voxel ? It doesnt seem so to me because i tried it over only two frames (3 reruns were done for two frames separately and a .trr which had these two frames only) and the numbers did not seem to be averages. Can someone help me in figuring out what is going on ? Amit On Tue, Jun 21, 2011 at 9:16 AM, Amit Choubey kgp.a...@gmail.com wrote: On Tue, Jun 21, 2011 at 1:13 AM, Jianguo Li ljg...@yahoo.com.sg wrote: Hi Amit, May I ask you a question? In your calculation of local pressure using a trajectory file, did you get a single averaged localpressure.dat file? Or else you get a bunch of separate files for each frame (e.g., localpressure.dat0, localpressure.dat1, localpressure.dat2 )? Yes I do get different files for different trajectories. All the files seem to have the same problem ie a very large/small number printed as tensor elements of the pressure for some of the voxels. Do you have such problems ? Could we compare our methodologies to use the local pressure version ? Amit Thank you very much! Cheers, Jianguo
Re: [gmx-users] How to exert different lateral pressure profile of a membrane to study its influence on a protein inserted in the double layer membrane?
Lateral pressure is a function of z-distance, maybe you can try simulations using different surface tension, which is the integration of lateral pressure. Cheers, Jianguo From: KONG Xian xiansh...@gmail.com To: gmx-users@gromacs.org Sent: Wednesday, 27 July 2011 10:58:56 Subject: [gmx-users] How to exert different lateral pressure profile of a membrane to study its influence on a protein inserted in the double layer membrane? Dear all: I am working on a research to study whether the Lateral pressure profile influence the protein function. To get different lateral pressure profile, I used Parinello-Rahman P coupling method and anisotropic pressure coupling with different p_ref values(such as 0.9bar, 1bar, 1.1bar, .,2bar) in xy. I wonder whether this method feasible. If it is not feasible, could anyone please give me a hint on how to do it. Thank you KONG Xian __ Information from ESET NOD32 Antivirus, version of virus signature database 6327 (20110726) __ The message was checked by ESET NOD32 Antivirus. http://www.eset.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] REMD with 'bad contacts' error
One thing you can try in your membrane simulation is to couple the Protein, Lipid and Water_Ion separately to the thermal bath. Cheers, Jianguo From: Sheeba Jem sheeba@googlemail.com To: gmx-users@gromacs.org Sent: Wednesday, 6 July 2011 07:05:43 Subject: [gmx-users] REMD with 'bad contacts' error Dear Gromacs users, I am having trouble running REMD for a system containing one peptide molecule on the surface of a lipid membrane, the system contains the following: Protein 1 POPC128 Water 4847 Na+ 9 Cl- 15 The total number of atoms in the system is 21483. I have 50 replicas with temperatures distributed from 250 to 400 K. After setting up the system I minimized and equilibrated the system for 14 ns at three temperatures: 250 K, 300K and 350 K. I take the output file from the 250 K run and use that as the starting structure for the temperatures between 250 to 300 K; similarly the output file from 300 K as the starting structure for replicas between 300 to 350 K and for the replicas between 350 to 400 K I use the output from the 350 K run. I further equilibrate these structures at the replica temperature for 10 ns. The output from these 10 ns runs are then used as starting structures for the replica exchange simulation. However when the replica exchange simulation begins to run, it crashes after 2 ps with a bad contact error: t = 2.008 ps: Water molecule starting at atom 21421 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Jul 4 18:07:21 2011 22666 4 7.04 handleTSRegisterTerm(): TS reports task 7 pid 15856 on hostcmp-13-9 killed or core dumped I use the Gromacs version 4.0.5 for all the simulations. Since the starting structure for each replica has been well equilibrated I am not sure how there could be hard contacts in the system. I looked at the input structures and the trajectories from the equilibration runs and I could not find anything strange with the system leading to hard contacts. Also the membrane remains intact for the high temperature replicas. Since I could not find anything to change in the system, I tried running REMD reducing the time step from 2 fs to 1 fs which also gave a similar error: t = 2.020 ps: Water molecule starting at atom 18919 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates I then tried with a timestep of 0.1 fs and got the same bad contacts error: t = 0.101 ps: Water molecule starting at atom 20251 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Jul 4 18:34:17 2011 25639 4 7.04 handleTSRegisterTerm(): TS reports task 5 pid 17349 on hostcmp-4-5 killed or core dumped I am not sure if reducing the timestep further would help therefore I looked at the temperature and pressure coupling. For all the above simulations I had used nose-hoover thermostat and a parrinello-rahman barostat with semi-isotropic pressure coupling. I had previously 'successfully' ran a REMD simulation of the peptide in water with isotropic coupling, the difference in the two .mdp files were the type of pressure coupling and changes in the bond contraint parameters (I have attached both the mdp files). Since semi-isotropic pressure coupling reproduces membrane properties well, I had used it for the peptide-lipid system. To see if changing the coupling type made a difference, with the 0.1 fs time step, I changed the coupling type to isotropic and this time the job crashed with the lincs warning: Step 2112, time 0.2112 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 1741.123129, max 74557.351562 (between atoms 5726 and 5727) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 5703 5704 46.50.1360 0.1954 0.1360 5702 5703 88.30.1430 0.3582 0.1430 5687 5688 92.20.1530 1.5410 0.1530 (a long list of angles..) I then ran REMD with the same mdp file I had used for the peptide water system changing only the temperature of the replicas accordingly and I still got the bad contacts error: t = 2.004 ps: Water molecule starting at atom 21424 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Jul 4 20:11:29 2011 31398 4 7.04 handleTSRegisterTerm(): TS reports task 5 pid 26543 on hostcmp-23-1 killed or core dumped I submit the REMD jobs with the following lines in a .lsf file #!/bin/tcsh -f #BSUB -J REMD #BSUB -x #BSUB -q 512cpu #BSUB -n 50 #BSUB -e err.%J #BSUB -o log.%J #BSUB -a mvapich mpirun /ifs1/apps/gromacs-405/bin/mdrun_mpi -s remd.tpr -multi 50 -replex 1000 -deffnm remd I am not sure where I am going wrong and
Re: [gmx-users] Energy-groups?
You can specify the energygrps in mdp file, grompp a new tpr file and use -rerun option of the mdrun to get a new edr file Cheers Jianguo From: nishap.pa...@utoronto.ca nishap.pa...@utoronto.ca To: gmx-users@gromacs.org Sent: Tuesday, 7 December 2010 02:56:04 Subject: [gmx-users] Energy-groups? Hello, I want to plot the interaction potential energy between my solute and solvent. In my .mdp file I did not mention anything under energygrps,so I am thinking it calculates the energies for the whole system. But is there a way I can extract say for example LJ-14 term between my solute and solvent using the same .edr file? Or would I have to specify my energygrps and run the simulation again. Thanks. Nisha --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] Re: local pressure v4.5 issues
Hi Amit, I also encountered the same problem you mentioned. In v4.5, when using -nstlp wiht large value (e.g., 1000), I got one file localpressure.dat0. I tested first several frames of a trajectory, the calculated pressure is not the average of the pressure of individual frames. Btw, did you use CHARMM FF in your simulations and how did you convert the tpr files from v 4.5 to v 4.0? Cheers Jianguo From: Amit Choubey kgp.a...@gmail.com To: Jianguo Li ljg...@yahoo.com.sg; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, 1 July 2011 10:32:07 Subject: Re: [gmx-users] Re: local pressure v4.5 issues Hello Everyone, The git version of local pressure calculation at http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure is broken. I could not get it to work for my simulations. I installed gromacs local pressure version 4.0 from ftp://ftp.gromacs.org/pub/tmp/ I used gromacs-4.0.2_localpressure.tar.gz in that folder. The pressure values printed using this version seem reasonable to me. I converted all the tpr files from v 4.5 to v 4.0. The output of the mdrun in v 4.0 is a single file localpressure.dat . On the contrary in v 4.5 there were separate localpressure.dat* files for each frame. I am not sure what exactly is the content of localpressure.dat. Does it have the time averaged value of pressure tensor for each voxel ? It doesnt seem so to me because i tried it over only two frames (3 reruns were done for two frames separately and a .trr which had these two frames only) and the numbers did not seem to be averages. Can someone help me in figuring out what is going on ? Amit On Tue, Jun 21, 2011 at 9:16 AM, Amit Choubey kgp.a...@gmail.com wrote: On Tue, Jun 21, 2011 at 1:13 AM, Jianguo Li ljg...@yahoo.com.sg wrote: Hi Amit, May I ask you a question? In your calculation of local pressure using a trajectory file, did you get a single averaged localpressure.dat file? Or else you get a bunch of separate files for each frame (e.g., localpressure.dat0, localpressure.dat1, localpressure.dat2 )? Yes I do get different files for different trajectories. All the files seem to have the same problem ie a very large/small number printed as tensor elements of the pressure for some of the voxels. Do you have such problems ? Could we compare our methodologies to use the local pressure version ? Amit Thank you very much! Cheers, Jianguo From: Amit Choubey kgp.a...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, 20 June 2011 07:08:03 Subject: [gmx-users] Re: local pressure v4.5 issues Dear all, I did another simulation with only SPC water. Then I used the local pressure gromacs to calculate the stresses. It seems to be reasonable. I am not sure how to figure out what goes wrong with my previous simulations when plugged into the local pressure gromacs. Could someone help me in figuring out whats the issue ? Thank You. On Fri, Jun 17, 2011 at 6:00 PM, Amit Choubey kgp.a...@gmail.com wrote: Dear all, I installed the git version of local pressure calculation from http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure The I invoked mdrun mdrun_lp -v -s rerun.tpr -g rerun_log -olp -rerun traj0.gro -localpgrid 0.1 This created a file named localpressure.dat0. This is a binary file so I could not look at it directly. I am not sure if there is a tool in the gromacs to look at it directly. To look at the data in localpressure.dat0 I used the planar_av.c code available in pressure-tools folder at http://md.chem.rug.nl/cgmartini/index.php/3d When I look at the Pressure tensor averaged over xy plane, some of the numbers are reasonable but few of them are ridiculously large numbers which is not expected. I checked this on two different simulations and I got the same problems. The simulations had run OK previously. Could someone help me in figuring our whats going on ? Amit Choubey -- 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: local pressure v4.5 issues
I downloaded v4.5 and v4.0 from the same websites as you mentioned in previous email. I am not sure why v4.5 give inconsistent results. I haven't try v4.0, because my simulation is using CHARMM FF. Could you give more details of conversion tpr files from v4.5 to v4.0 using CHARMM FF? Thank you very much! Cheers, Jianguo From: Amit Choubey kgp.a...@gmail.com To: Jianguo Li ljg...@yahoo.com.sg Cc: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, 1 July 2011 11:47:58 Subject: Re: [gmx-users] Re: local pressure v4.5 issues On Thu, Jun 30, 2011 at 7:57 PM, Jianguo Li ljg...@yahoo.com.sg wrote: Hi Amit, I also encountered the same problem you mentioned. In v4.5, when using -nstlp wiht large value (e.g., 1000), I got one file localpressure.dat0. I tested first several frames of a trajectory, the calculated pressure is not the average of the pressure of individual frames. In v4.5 it outputs the profile for frames in separate files which is ok. My concern is what exactly is going in v 4.0 where there is only one file for all the frames. Also where did you download v4.5 and v4.0 from ? Btw, did you use CHARMM FF in your simulations and how did you convert the tpr files from v 4.5 to v 4.0? Yes i have used CHARMM FF and i will have to figure out the conversion. Cheers Jianguo From: Amit Choubey kgp.a...@gmail.com To: Jianguo Li ljg...@yahoo.com.sg; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, 1 July 2011 10:32:07 Subject: Re: [gmx-users] Re: local pressure v4.5 issues Hello Everyone, The git version of local pressure calculation at http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure is broken. I could not get it to work for my simulations. I installed gromacs local pressure version 4.0 from ftp://ftp.gromacs.org/pub/tmp/ I used gromacs-4.0.2_localpressure.tar.gz in that folder. The pressure values printed using this version seem reasonable to me. I converted all the tpr files from v 4.5 to v 4.0. The output of the mdrun in v 4.0 is a single file localpressure.dat . On the contrary in v 4.5 there were separate localpressure.dat* files for each frame. I am not sure what exactly is the content of localpressure.dat. Does it have the time averaged value of pressure tensor for each voxel ? It doesnt seem so to me because i tried it over only two frames (3 reruns were done for two frames separately and a .trr which had these two frames only) and the numbers did not seem to be averages. Can someone help me in figuring out what is going on ? Amit On Tue, Jun 21, 2011 at 9:16 AM, Amit Choubey kgp.a...@gmail.com wrote: On Tue, Jun 21, 2011 at 1:13 AM, Jianguo Li ljg...@yahoo.com.sg wrote: Hi Amit, May I ask you a question? In your calculation of local pressure using a trajectory file, did you get a single averaged localpressure.dat file? Or else you get a bunch of separate files for each frame (e.g., localpressure.dat0, localpressure.dat1, localpressure.dat2 )? Yes I do get different files for different trajectories. All the files seem to have the same problem ie a very large/small number printed as tensor elements of the pressure for some of the voxels. Do you have such problems ? Could we compare our methodologies to use the local pressure version ? Amit Thank you very much! Cheers, Jianguo From: Amit Choubey kgp.a...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, 20 June 2011 07:08:03 Subject: [gmx-users] Re: local pressure v4.5 issues Dear all, I did another simulation with only SPC water. Then I used the local pressure gromacs to calculate the stresses. It seems to be reasonable. I am not sure how to figure out what goes wrong with my previous simulations when plugged into the local pressure gromacs. Could someone help me in figuring out whats the issue ? Thank You. On Fri, Jun 17, 2011 at 6:00 PM, Amit Choubey kgp.a...@gmail.com wrote: Dear all, I installed the git version of local pressure calculation from http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure The I invoked mdrun mdrun_lp -v -s rerun.tpr -g rerun_log -olp -rerun traj0.gro -localpgrid 0.1 This created a file named localpressure.dat0. This is a binary file so I could not look at it directly. I am not sure if there is a tool in the gromacs to look at it directly. To look at the data in localpressure.dat0 I used the planar_av.c code available in pressure-tools folder at http://md.chem.rug.nl/cgmartini/index.php/3d When I look at the Pressure tensor averaged over xy plane, some of the numbers are reasonable but few of them are ridiculously large numbers which is not expected. I checked this on two different simulations and I got the same problems. The simulations had run OK
Re: [gmx-users] Re: local pressure v4.5 issues
How large is the number? Does the large number converges? Lateral pressure is usually large (positive or negative) at the water-hydrophobic interface. e.g., see figures in this paper: J. Am. Chem. Soc. 2011, 133, 3720–3723. Cheers, Jianguo From: Amit Choubey kgp.a...@gmail.com To: Jianguo Li ljg...@yahoo.com.sg; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, 22 June 2011 00:16:43 Subject: Re: [gmx-users] Re: local pressure v4.5 issues On Tue, Jun 21, 2011 at 1:13 AM, Jianguo Li ljg...@yahoo.com.sg wrote: Hi Amit, May I ask you a question? In your calculation of local pressure using a trajectory file, did you get a single averaged localpressure.dat file? Or else you get a bunch of separate files for each frame (e.g., localpressure.dat0, localpressure.dat1, localpressure.dat2 )? Yes I do get different files for different trajectories. All the files seem to have the same problem ie a very large/small number printed as tensor elements of the pressure for some of the voxels. Do you have such problems ? Could we compare our methodologies to use the local pressure version ? Amit Thank you very much! Cheers, Jianguo From: Amit Choubey kgp.a...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, 20 June 2011 07:08:03 Subject: [gmx-users] Re: local pressure v4.5 issues Dear all, I did another simulation with only SPC water. Then I used the local pressure gromacs to calculate the stresses. It seems to be reasonable. I am not sure how to figure out what goes wrong with my previous simulations when plugged into the local pressure gromacs. Could someone help me in figuring out whats the issue ? Thank You. On Fri, Jun 17, 2011 at 6:00 PM, Amit Choubey kgp.a...@gmail.com wrote: Dear all, I installed the git version of local pressure calculation from http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure The I invoked mdrun mdrun_lp -v -s rerun.tpr -g rerun_log -olp -rerun traj0.gro -localpgrid 0.1 This created a file named localpressure.dat0. This is a binary file so I could not look at it directly. I am not sure if there is a tool in the gromacs to look at it directly. To look at the data in localpressure.dat0 I used the planar_av.c code available in pressure-tools folder at http://md.chem.rug.nl/cgmartini/index.php/3d When I look at the Pressure tensor averaged over xy plane, some of the numbers are reasonable but few of them are ridiculously large numbers which is not expected. I checked this on two different simulations and I got the same problems. The simulations had run OK previously. Could someone help me in figuring our whats going on ? Amit Choubey -- 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 calcuation for Gromacs-4.5
Dear all, I have made a test calculation of local pressure using version 4.5 for my membrane simulation using CHARMM FF. When rerun the simulation, mdrun gives the localpressure data. Howeve, instead of giving an anveraged data of the local pressure, mdrun gives a separate file for each frame, so I got many files: localpressure.dat0, localpressure.dat1, localpressure.dat2, localpressure.dat3 .. Then I need to calculate the pressure tensor for each frame and make average. but these localpressure.dat files are very big (each file is about 30 Mb), occupying large space of the hard disk. Can anyone give some suggestions on how to fix this? Thank you very much! The command is: mdrun_d -s lp.tpr -rerun box_md5.trr -x box_md5_rerun.xtc -o box_md5_rerun.trr -g md5_rerun.log -localpgrid 0.1 And the output message is: Dumping local pressure based on 1 frames to localpressure.dat0... Reading frame 2 time 119400.000 Dumping local pressure based on 1 frames to localpressure.dat1... Reading frame 3 time 119500.000 Dumping local pressure based on 1 frames to localpressure.dat2... Reading frame 4 time 119600.000 Dumping local pressure based on 1 frames to localpressure.dat3... Reading frame 5 time 119700.000 Dumping local pressure based on 1 frames to localpressure.dat4... Reading frame 6 time 119800.000 ... Cheers, Jianguo From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, 10 June 2011 07:10:35 Subject: Re: [gmx-users] local pressure calcuation for Gromacs-4.5 Amit Choubey wrote: Thanks Justin, I tried to install the recent git version but the configure file is missing. How should I install this version ? Run the bootstrap script. It generates the configure script. -Justin On Thu, Jun 9, 2011 at 12:45 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Amit Choubey wrote: Dear all, I saw an unanswered post at http://lists.gromacs.org/pipermail/gmx-users/2011-January/058063.html It is about calculating local pressure in v 4.5 when using CHARMM FF. Could someone give me some pointers about this? I don't know what the development status of version 4.5 is, but you can access it at: http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure It hasn't been merged with release-4-5-patches in some time, so many resolved bugs won't be fixed. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto: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 the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] gmx4.5.4 installation help
The error message already shows some hints. Try recompile FFTW with -fPIC. Jianguo From: Chandan Choudhury iitd...@gmail.com To: gmx-users gmx-users@gromacs.org Sent: Thursday, 2 June 2011 15:03:03 Subject: [gmx-users] gmx4.5.4 installation help Hello gmx-users, I am trying to install gmx-4.5.4 on a HPC Linux cluster x86_64. 1. I installed fftw 3.2.2 ./configure --prefix /soft/sudip/abc/execs/fftw/ --enable-single --enable-threads 2. Installing Gromacs : CPPFLAGS and LDFLAGS were written in bashrc file a) ./configure --prefix=/soft/sudip/abc/execs/gromacs/ execute successfully without any complain. b) make /usr/bin/ld: /soft/sudip/abc/execs/fftw/lib/libfftw3f.a(apiplan.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /soft/sudip/abc/execs/fftw/lib/libfftw3f.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[3]: *** [libmd.la] Error 1 make[3]: Leaving directory `/soft/sudip/abc/untar/gromacs-4.5.4/src/mdlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/soft/sudip/abc/untar/gromacs-4.5.4/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/soft/sudip/abc/untar/gromacs-4.5.4/src' make: *** [all-recursive] Error 1 shows problem. Couldnot understand the origin of problem. Kndly let me know if some information is missing. Chandan -- Chandan kumar Choudhury NCL, Pune 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
Re: [gmx-users] Gravity force in equation of motion
Seems gravity is much weaker than the other forces in molecular simulations and thus can be neglected. Jianguo From: mohsen ramezanpour ramezanpour.moh...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, 1 June 2011 15:20:09 Subject: [gmx-users] Gravity force in equation of motion Dear All There is a question about applied forces in MD equations of motion. Where do we insert Gravity in our equation? In the other words : Had we ignored gravity force in our equations? Why? Actually I read manual but I weren't answered. Thanks in advance -- 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] Improper dihedrals in Charmm FF
Dear all, My molecule contains -CH=CH- fragment and I am trying to create the topology using Charmm FF. It seems that there is no improper dihedrals for -CH=CH- fragment in Charmm FF, while other FF (e.g., Amber or OPLS) has additional improper dihedrals terms for that fragment. Could anybody confirm this? Thanks very much! Cheers, 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
Re: [gmx-users] C-terminal amidation of peptide
If you use CHARMM FF and Gromacs4.5 or later, you can use -ter in pdb2gmx and choose CT2 to add NH2 at C-terminus. For other FF, you may need to manually add NH2 in pdb file. Jianguo From: anna Kalkbrenner anna.kalkbren...@gmail.com To: gmx-users@gromacs.org Sent: Sunday, 20 March 2011 11:59:34 Subject: [gmx-users] C-terminal amidation of peptide Hello, I'm sorry if my questions are on the elementary level, as I am still learning how to use GROMACS. I would like perform an MD run on a peptide that has an amidated c-terminal. My understanding is that I can modify my PDB structure to include the NH2 group. Then, with pdb2gmx I use the -ter option and select none for the C-terminus. Is this correct? What is the best way to edit the PDB file to add the amide group? Can it be done through a structural editor? Best regards, Anna -- 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: g_hbond output
If I understand correctly, $2 is the number of hydrogen bonds defined by cutoff distance and the cutoff angle. $3 is the number of pairs within the cutoff distance, but beyond the cutoff angle. You may got different number of hbonds using different cutoff distance and cutoff angle. Jianguo From: ZHAO Lina lnzha...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, 16 March 2011 13:33:57 Subject: [gmx-users] Re: g_hbond output @ legend length 2 @ s0 legend Hydrogen bonds @ s1 legend Pairs within 0.35 nm 0 0 0 200 0 0 400 2 1 600 0 3 800 0 2 1000 1 0 : 5 3 2 Here the situations, what's the $2 and $3 mean, why when $1=1000, $3=0 if the $3 means pairs. I tried pymol, and on the last frame, there were 4 hydrogen bonds, between 7 residues. it's different from here 3 2 Thanks and sorry for last email without my realization it sent. lina -- 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: g_hbond output
A pair within the cutoff distance (e.g., 0.35nm) either belongs to $2 or $3, but cannot belong to both columns. If the program finds a pair shorter than 0.35nm, and the angle is smaller than 30deg., then the program put this pair in the column 2. If the program finds a pair shorter than 0.35nm, and the angle is larger than 30deg., then the program put this pair in the column 3. Jianguo From: ZHAO Lina lnzha...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, 16 March 2011 15:31:30 Subject: Re: [gmx-users] Re: g_hbond output s0 legend Hydrogen bonds @ s1 legend Pairs within 0.35 nm 0 0 0 200 0 0 400 2 1 600 0 3 800 0 2 1000 1 0 Here is my question, since there is already one bond formed, then why there is none pairs in 1000? On Wed, Mar 16, 2011 at 3:16 PM, Jianguo Li ljg...@yahoo.com.sg wrote: If I understand correctly, $2 is the number of hydrogen bonds defined by cutoff distance and the cutoff angle. $3 is the number of pairs within the cutoff distance, but beyond the cutoff angle. You may got different number of hbonds using different cutoff distance and cutoff angle. Jianguo From: ZHAO Lina lnzha...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, 16 March 2011 13:33:57 Subject: [gmx-users] Re: g_hbond output @ legend length 2 @ s0 legend Hydrogen bonds @ s1 legend Pairs within 0.35 nm 0 0 0 200 0 0 400 2 1 600 0 3 800 0 2 1000 1 0 : 5 3 2 Here the situations, what's the $2 and $3 mean, why when $1=1000, $3=0 if the $3 means pairs. I tried pymol, and on the last frame, there were 4 hydrogen bonds, between 7 residues. it's different from here 3 2 Thanks and sorry for last email without my realization it sent. lina -- 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] Zero Potential of Mean Force with g_wham
I met the same problem when using 4.5.1 for some systems, the PMF shows zero curve, while the hist file looks fine. The problem disappears when using 4.5.2. Jianguo From: Susana Tomasio susietoma...@gmail.com To: gmx-users@gromacs.org Sent: Wednesday, 9 March 2011 20:07:25 Subject: [gmx-users] Zero Potential of Mean Force with g_wham Dear all, I am running umbrella sampling of a molecule through a lipid bilayer with gromacs 4.5.1. When I extracted the potential of mean force with g_wham I got zero for all the windows. Any ideas of why this is happening? This is the command I used: g_wham_4.5.1 -it tpr.dat -if pullf.dat -o -hist And this is the pull code of my .mdp file: ; Pull code pull = umbrella pull_geometry = position pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = Bilayer pull_group1 = Protein pull_vec1 = 0 0 0 pull_init1 = 0 0 0 pull_rate1 = 0 pull_pbcatom0 = 1453 pull_pbcatom1 = 13187 pull_k1 = 3000 ; kJ mol^-1 nm^-2 pull_nstxout = 1000 ; every 2 ps pull_nstfout = 1000 ; every 2 ps Thank you. Best regards, Susana -- 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] parallel running
You don't use qsub or bsub? usually you should submit a script file containing the gromacs command, then bsub/qsub will allocate the required resource to your job. Jianguo From: mohsen ramezanpour ramezanpour.moh...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, 8 March 2011 17:26:19 Subject: [gmx-users] parallel running Dear All I want to run gromacs in parallel on cluster.for this I follow below steps: 1-I connect to a node with ssh comand,fro example: ssh compute-o-1 2-cd scratch 3-grompp -f md.mdp-c input.gro-o output.tpr -p topol.top -n index.ndx 4- nohup mpirun -np 8 mdrun -deffnm output The result is running mdrun on one node(compute-0-1) (on its 4 CPUs) Besides when I used the following command I get an executeable Error: mpirun -np 8 mdrun_mpi -deffnm output The Error is related to mdrun_mpi I think is related to my cluster,because both of above commands work in my laptop Please let me know how can I run mdrun on all of CPUs of my cluster. Thanks in advance Mohsen -- 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 simulation of peptide-membrane system
Dear all, I'd like to do folding simulations of a short peptide on membrane surface using REMD using atomistic FF. But the problem is that membrane will disrupt at high temperatures. To maintain the membrane structure, I am thinking the following two methods: (1) To use different coupling temperature for different groups (e.g., keeping membrane at 323K for all the replicas, but keeping peptide and water with different temperatures). Will this lead to artifact? (2) If this leads to serious artifact, I may need to use constraints on the membrane, as mentioned in the paper from Berkowitz group. Is there any other method for the above problem? Any comments is greatly appreciated, thank you in advance, Cheers, 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
Re: [gmx-users] Re: adding ff parameter of modified residue to charmm ff
My way of doing it is: (1) add two new residues entries (with two different names) for glycine and seine in the rtp file and corresponding FF files. The new entries in the rtp file for glycine and serine should have the same number of atoms as in the real molecule (delete the unnecessary H or OH groups if needed) (2) then use pdb2gmx (3) then manually construct the bond, angle and dihedrals at the linkage site. Cheers, Jianguo From: bharat gupta bharat.85.m...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, 3 March 2011 11:31:38 Subject: [gmx-users] Re: adding ff parameter of modified residue to charmm ff Hi, I followed the tutorial - http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field for updating the Charmm FF for my modified residue .. I added the residues to the .rtp file , then I added the new atom types in .atp file , The compound has some linkage with serine and glycine ... I want to know how and where shall I add the linkage parameters and the parameters (in bits) given below (The parameter file of the compound looks like this ) .. BONDS ! !V(bond) = Kb(b - b0)**2 ! !Kb: kcal/mole/A**2 !b0: A ! !atom type Kb b0 CA1 CA2 305.00 1.3750 ! CA2 CA3 305.00 1.3750 ! CA3 CA4 305.00 1.3750 ! HPc CA1 340.000 1.08 ! HPc CA2 340.000 1.08 ! HPc CA3 340.000 1.08 ! HPc CA4 340.000 1.08 ! ANGLES ! !V(angle) = Ktheta(Theta - Theta0)**2 ! !V(Urey-Bradley) = Kub(S - S0)**2 ! !Ktheta: kcal/mole/rad**2 !Theta0: degrees !Kub: kcal/mole/A**2 (Urey-Bradley) !S0: A ! !atom types KthetaTheta0 Kub S0 ! NR2c CP2c NR1c 130.00114.00 ! CP2c NR2c CP1c 130.00106.00 ! CP2c NR1c CP1c 130.00107.90 ! NR2c CP1c CP1c 130.00108.30 ! NR2c CP1c CE1c 45.80129.50 ! NR1c CP1c OcH42.00126.00 ! NR1c CP1c CP1c 130.00103.00 ! !Connection to the ser fragment !-- CT2 CT1 CP2c52.000 108. ! ALLOW ALI PEP POL ARO HB CT1 CP2c 50.000 109.5000 ! ALLOW PEP NH1 CT1 CP2c 50.000 107. ! ALLOW PEP POL ARO ALI NR2C CP2C CT1 40.00125.00 ! !Connection to the gly fragment !-- NR1C CT2 C 50.000 107. NR1c CT2 HB 48.000 108. CP2C NR1C CT2 36.00129.00 CP1C NR1C CT2 32.00123.40 ! DIHEDRALS ! !V(dihedral) = Kchi(1 + cos(n(chi) - delta)) ! !Kchi: kcal/mole !n: multiplicity !delta: degrees ! !atom types Kchin delta ! CP2C NR2C CP1C CP1C14. 2 180.00 ! CP2C NR1C CP1C CP1C14. 2 180.00 ! NR2C CP2C NR1C CP1C14. 2 180.00 ! NR2C CP1C CP1C NR1C 4. 2 180.00 ! NR1C CP2C NR2C CP1C 4. 2 180.00 ! CA1 CA2 CA3 CA4 3.1000 2 180.00 ! !barrier CA-CB CP1C CP1C CE1C HA1C 6.84 2 180.00 ! CP1C CP1C CE1C CA1 6.84 2 180.00 ! NR2C CP1C CE1C HA1C 6.84 2 180.00 ! NR2C CP1C CE1C CA1 6.84 2 180.00 ! ! !barrier CB-CG2 CP1C CE1C CA1 CA2 1.4 2 180.00 ! HA1C CE1C CA1 CA2 1.4 2 180.00 ! ! CP2C NR1C CP1C OCH 14.002 180.00 ! NR2C CP2C NR1C CT2 14.002 180.00 ! NR2C CP1C CP1C OCH 14.002 180.00 ! CP1C NR1C CP2C CT1 14.002 180.00 ! OCH CP1C NR1C CT2 14.002 180.00 ! CP1C NR2C CP2C CT1 14.002 180.00 ! CP1C CP1C NR1C CT2 14.002 180.00 ! CT1 CP2C NR1C CT2 14.002 180.00 ! ! ! Linking the chromophore and the glycine fragment OCCT2 NR1C 0. 1 0.00 ! NH1 CCT2 NR1c 0.6000 1 0.00 ! CP2C NR1C CT2 HB 0.032 3 0.00 ! CP2c NR1c CT2 C 0.032 3 0.00 ! CP1c NR1c CT2 HB 0.032 3 180.00 ! CP1c NR1c CT2 C 0.032 3 180.00 ! ! ! Linking the chromophore and the serine fragment CNH1 CT1 CP2C 0.2000 1 180.00 ! HNH1 CT1 CP2C 0. 1 0.00 ! NR2C CP2C CT1 HB 0.105 3 180.00 ! NR2C CP2C CT1 NH10.105 3 180.00 ! NR2C CP2C CT1 CT20.105 3 180.00 ! NR1C CP2C CT1 HB 0.105 3 0.00 ! IMPROPER ! !V(improper) = Kpsi(psi - psi0)**2 ! !Kpsi: kcal/mole/rad**2 !psi0: degrees !note that the second column of numbers (0) is ignored ! !atom types Kpsi psi0 ! CP2C NR2C NR1C CT1 0.5 0 0.00 CP2C NR1C NR2C CT1 0.5 0 0.00 ! CP1C NR1C CP1C OCH 0.5 0 0.00 CP1C CP1C NR1C OCH 0.5 0 0.00 ! NR1C CP1C CP2C CT2 0.45 0 0.00 NR1C CP2C CP1C CT2 0.45 0 0.00 ! CP1C NR2C CP1C CE1C 220.0 0 0.00 CP1C CP1C NR2C CE1C 220.0 0 0.00 ! !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] ! !epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) !Rmin/2: A, Rmin,i,j =
Re: [gmx-users] Can g_wham support using different temperature for different windows?
Thanks for your comments, Patric. You are right. The energy barrier is too high for charged groups to translocate the hydrophobic region of the membrane. And my peptide contains 12 positively charge residues (ARG and LYS), therefore it is unlikely to sample those translocation. I am considering to extend my simulations to microsecond level or longer or use REMD. Cheers, Jianguo From: Patrick Fuchs patrick.fu...@univ-paris-diderot.fr To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, 23 February 2011 19:04:05 Subject: Re: [gmx-users] Can g_wham support using different temperature for different windows? Hi, I think your PMF is asymetric because your peptide is asymetric and you don't sample enough. To get a symetric PMF, your peptide would have to sample all the possible conformations *and* orientations in each window. Thus it means that for the windows in the center of the bilayer (where you say it's extended and interacts with the two monolayers) it'll have to rotate completely the other way round. This event will probably be *very* rare because you have to translocate positive charges across the membrane which cost ~ 40 to 50 kJ/mol (see the PMF of Lys+ and Arg+ in 10.1021/ct700324x). So as suggested by Chris, Justin and Xavier, you'll have to sample way more than 100 ns per window. I think you should go at least to the microsecond time scale (or more?). Or maybe starting from different initial conformations/orientations for a given window and then concatenate the different trajectories? Also consider the remark of Xavier, TM or interfacial peptides are most of the time alpha-helical within the membrane. So far in literature, PMFs of a whole peptide across a bilayer were done by restraining the peptide in a helical conformation (e.g. 10.1016/j.bpj.2010.12.3682). It is anyway a very difficult problem (and probably impossible at atomistic resolution) to get a converged PMF for a whole peptide (e.g. 10.1016/j.bpj.2009.03.059). Ciao, Patrick Le 23/02/2011 05:25, Jianguo Li a écrit : Sorry, why do you think the PMF should be asymmetric? I pulled my peptide from d=9nm (above the membrane) to d=-3nm (below the membrane) and I did windowed umbrella sampling in the range of d=-1.05nm to d=9nm. At least the PMF should be symmetric with respect of the bilayer center in the range of d=[-1.05nm 1.05nm], something like a guassian distribution. But I got asymmetric PMF in this region. I also did reverse pulling starting from the peptide below the membrane ending with the peptide above the membrane. And the subsequent PMF of reversed pulling is also asymmetic. I have position restrains of the phosphate beads of the lipids in z-direction. So the membrane should be stable in REMD. But as you mentioned, if peptide is truly stuck in this orientation, REMD may be not useful. I will do a single simulation first at a higher temperature (e.g., 400K) in those bad windows to see if the peptide conformations are fully sampled. Cheers, Jianguo *From:* Justin A. Lemkul jalem...@vt.edu *To:* Gromacs Users' List gmx-users@gromacs.org *Sent:* Wednesday, 23 February 2011 10:24:46 *Subject:* Re: [gmx-users] Can g_wham support using different temperature for different windows? Jianguo Li wrote: Thank you, Justin. Actually I did windowed umbrella simulations from d=-1.05nm to d=9nm. Since I think there is no problem in the region out of the membrane, so I only show the configurations within the membrane. My objective is to access the free energy barrier of the peptide translocate the negatively charged membrane. The problem is that the PMF is not symmetric with respect to the bilayer center due to the unconverged simulations. I would argue that the PMF is not symmetric because your reaction coordinate is not symmetric. How can you calculate a free energy of crossing a charged membrane when your peptide does not cross the membrane? What I proposed earlier was to obtain configurations at equal distances above and below the membrane (arbitrary in a periodic system, but hopefully you get the idea). If you can extract the peptide to the point where it is liberated from the membrane in the negative direction, I'd suspect you could solve your problem. Since g_wham does not support different temperatures in different windows, to increase the converges, I will probably consider to do REMD in those bad windows. This technique might work, provided you don't destabilize the membrane, but if the peptide is truly stuck in this orientation, I doubt that limited-range REMD would be very useful. -- 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
Re: [gmx-users] Can g_wham support using different temperature for different windows?
Dear all, Thank you all for your suggestions or comments to my problem. Now I am planning to extend my simulations or using REMD in those bad windows to get converged PMF. I have another question: if I extend the umbrellar simulation to 1 microsecond only in those problematic windows, while running shorter simulation (e.g., 100 ns) in those windows far away from the membrane. Does g_wham accpet using diffrent simulation time for different windows? Thank you in again, Cheers, Jianguo From: XAvier Periole x.peri...@rug.nl To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, 23 February 2011 20:59:18 Subject: 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
Re: [gmx-users] Can g_wham support using different temperature for different windows?
Sorry I forgot to attach my mdp files. Here is the mdp file for pulling simulaition: - title= Martini cpp = /usr/bin/cpp define = -DPOSRES_LIP integrator = md ; start time and timestep in ps tinit= 0.0 dt = 0.02 nsteps = 500 ; number of steps for center of mass motion removal = nstcomm = 10 comm-grps= nstxout = 5000 nstvout = 50 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 1000 nstenergy= 1000 ; Output frequency and precision for xtc file = nstxtcout= 1000 xtc_precision= 100 nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist= 1.4 coulombtype = PME rcoulomb = 1.4 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon_r= 15 ; Method for doing Van der Waals = vdw_type = Shift ; cut-off lengths= rvdw_switch = 0.9 rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = No ; Temperature coupling = tcoupl = V-rescale ; Groups to couple separately = tc-grps = Protein_lipid Sol_Ion ; Time constant (ps) and reference temperature (K) = tau_t= 1.5 1.5 ref_t= 310 310 ; Pressure coupling = Pcoupl = Parrinello-Rahman Pcoupltype = semiisotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p= 10.0 10.0 compressibility = 3e-5 3e-5 ref_p= 1.0 1.0 constraints = none ; Type of constraint algorithm = constraint_algorithm = Lincs ; Do not constrain the start configuration = unconstrained_start = no ; Highest order in the expansion of the constraint coupling matrix = lincs_order = 4 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs_warnangle = 90 ; pull staff ; pull staff pull= umbrella pull_geometry = position pull_vec1= 0 0 -1 pull_dim = N N Y pull_start = no ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = lipid1 pull_group1 = Protein pull_init1 = 0.0 0.0 4.50 pull_rate1 = 0.001 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 Here is the pull part of the mpd file for the windowed umbrella sampling simulation, other part of the mdp file are same as that of pulling simulation. pull= umbrella pull_geometry = position pull_vec1= 0 0 -1 pull_dim = N N Y pull_start = no ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = lipid1 pull_group1 = Protein pull_init1 = 0.0 0.0 1.2 pull_k1 = 1000 ; kJ mol^-1 nm^-2 Cheers, Jianguo From: Jianguo Li ljg...@yahoo.com.sg To: jalem...@vt.edu; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, 22 February 2011 14:27:34 Subject: Re: [gmx-users] Can g_wham support using different temperature for different windows? Thanks Justin and Chris and sorry for confusing interpretation. Let me make it more clear. My peptide is flexible Martini beads, and highly positively charged. My membrane is a mixture of negatively charged lipids (25%) and zitterionic lipids(75%). So there is strong electrostatic attraction between peptide and membrane. To get the PMF, I did the following: (1) I did pulling simulation along (0 0 -1) direction to pull my peptide across the membrane. Then I got different configurations corresponding to different windows along the reaction coordinates, which is the z-distance between peptide and membrane. This figure (http://www.flickr.com/photos/lijg/5467080971/) shows some of the configurations at certain reaction coordinates. (2) In each window, I used the corresponding configuration that generated by the pulling simulation as initial input and run umbrella sampling. The size of each window is 0.15 nm, but close to the bilayer cneter (e.g., -0.6d0.6), I have increased number of windows so that the width of the window is to be 0.05 or 0.1 nm, I also tried to use different force
Re: [gmx-users] Can g_wham support using different temperature for different windows?
Thank you, Justin. Actually I did windowed umbrella simulations from d=-1.05nm to d=9nm. Since I think there is no problem in the region out of the membrane, so I only show the configurations within the membrane. My objective is to access the free energy barrier of the peptide translocate the negatively charged membrane. The problem is that the PMF is not symmetric with respect to the bilayer center due to the unconverged simulations. Since g_wham does not support different temperatures in different windows, to increase the converges, I will probably consider to do REMD in those bad windows. Cheers Jianguo From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Tuesday, 22 February 2011 21:10:08 Subject: Re: [gmx-users] Can g_wham support using different temperature for different windows? Jianguo Li wrote: Thanks Justin and Chris and sorry for confusing interpretation. Let me make it more clear. My peptide is flexible Martini beads, and highly positively charged. My membrane is a mixture of negatively charged lipids (25%) and zitterionic lipids(75%). So there is strong electrostatic attraction between peptide and membrane. To get the PMF, I did the following: (1) I did pulling simulation along (0 0 -1) direction to pull my peptide across the membrane. Then I got different configurations corresponding to different windows along the reaction coordinates, which is the z-distance between peptide and membrane. This figure (http://www.flickr.com/photos/lijg/5467080971/) shows some of the configurations at certain reaction coordinates. Are you not sampling configurations outside of the membrane (i.e. in water)? I would think that would solve your problem. You don't show any configurations in which the peptide is completely dissociated from the membrane. I don't know your objectives, but I would think that if you could completely extract the peptide from the membrane after passing through it, this would solve your problem. (2) In each window, I used the corresponding configuration that generated by the pulling simulation as initial input and run umbrella sampling. The size of each window is 0.15 nm, but close to the bilayer cneter (e.g., -0.6d0.6), I have increased number of windows so that the width of the window is to be 0.05 or 0.1 nm, I also tried to use different force constant in these windows. From the figure (http://www.flickr.com/photos/lijg/5467080971/) , we can classify the peptide conformation to be either extended (interacting with two bilayers) or compact (interacting with only one bilayer). Ideally, the peptide conformation should be similar for d=x and d=-x. The problem is that the configuration of peptide is not symmetric with respect to the bilayer center. For example, the peptide configuration is compact at d=0.6 and d=0.9, but the peptide is extended at d=-0.6 and d=-0.9. This leads Hysteresis. If I use g_wham to generate PMF, then the PMF is not symmetric with respect to the bilayer center. Using more number of windows and different force constant did not remove the problem. In my opinion, at least in some windows, the peptide should sample both compact and extended structure. But what I found is that the windowed Don't pre-judge the model :) Also, as I said before, there is no reason to suspect that MARTINI will produce any meaningful secondary structure changes. It was not parameterized to do so. umbrella simulation depends on the initial peptide conformation. If the initial peptide conformation is compact, then after 100 ns, it is still compact; if the initial peptide in that window is extended, the final configuration is also extended. I also tried to run longer equilibrium time (e.g., 200 ns), but the problem still exists. Sounds like a limitation of the force field model. My question is how to increase sampling of the peptide conformation? I just think of two choices: (1) use high temperature (e.g., 500K) at those bad windows. As I mentioned, I am wondering if g_wham can unbias the effect of using different temperatures in different windows. (2) use REMD in those bad windows. These need a lot of computational resources. Neither of these will be useful in generating a sensible PMF curve. WHAM needs a single temperature for proper weighting. If you start including different temperatures in different regions of phase space, I would imagine the weighting would be completely incorrect. Note that SMD is not the only option for generating starting configurations. If you think that certain orientations or configurations are correct, you can build them yourself, but keep in mind that you'll have to justify this procedure to a skeptical audience. -Justin Is there any other method to deal with the insufficient sampling? Any suggestions are welcome, thanks for your time reading this email! Cheers, Jianguo
Re: [gmx-users] Can g_wham support using different temperature for different windows?
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. 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 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?
Sorry, why do you think the PMF should be asymmetric? I pulled my peptide from d=9nm (above the membrane) to d=-3nm (below the membrane) and I did windowed umbrella sampling in the range of d=-1.05nm to d=9nm. At least the PMF should be symmetric with respect of the bilayer center in the range of d=[-1.05nm 1.05nm], something like a guassian distribution. But I got asymmetric PMF in this region. I also did reverse pulling starting from the peptide below the membrane ending with the peptide above the membrane. And the subsequent PMF of reversed pulling is also asymmetic. I have position restrains of the phosphate beads of the lipids in z-direction. So the membrane should be stable in REMD. But as you mentioned, if peptide is truly stuck in this orientation, REMD may be not useful. I will do a single simulation first at a higher temperature (e.g., 400K) in those bad windows to see if the peptide conformations are fully sampled. Cheers, Jianguo From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Wednesday, 23 February 2011 10:24:46 Subject: Re: [gmx-users] Can g_wham support using different temperature for different windows? Jianguo Li wrote: Thank you, Justin. Actually I did windowed umbrella simulations from d=-1.05nm to d=9nm. Since I think there is no problem in the region out of the membrane, so I only show the configurations within the membrane. My objective is to access the free energy barrier of the peptide translocate the negatively charged membrane. The problem is that the PMF is not symmetric with respect to the bilayer center due to the unconverged simulations. I would argue that the PMF is not symmetric because your reaction coordinate is not symmetric. How can you calculate a free energy of crossing a charged membrane when your peptide does not cross the membrane? What I proposed earlier was to obtain configurations at equal distances above and below the membrane (arbitrary in a periodic system, but hopefully you get the idea). If you can extract the peptide to the point where it is liberated from the membrane in the negative direction, I'd suspect you could solve your problem. Since g_wham does not support different temperatures in different windows, to increase the converges, I will probably consider to do REMD in those bad windows. This technique might work, provided you don't destabilize the membrane, but if the peptide is truly stuck in this orientation, I doubt that limited-range REMD would be very useful. -Justin Cheers Jianguo *From:* Justin A. Lemkul jalem...@vt.edu *To:* Gromacs Users' List gmx-users@gromacs.org *Sent:* Tuesday, 22 February 2011 21:10:08 *Subject:* Re: [gmx-users] Can g_wham support using different temperature for different windows? Jianguo Li wrote: Thanks Justin and Chris and sorry for confusing interpretation. Let me make it more clear. My peptide is flexible Martini beads, and highly positively charged. My membrane is a mixture of negatively charged lipids (25%) and zitterionic lipids(75%). So there is strong electrostatic attraction between peptide and membrane. To get the PMF, I did the following: (1) I did pulling simulation along (0 0 -1) direction to pull my peptide across the membrane. Then I got different configurations corresponding to different windows along the reaction coordinates, which is the z-distance between peptide and membrane. This figure (http://www.flickr.com/photos/lijg/5467080971/) shows some of the configurations at certain reaction coordinates. Are you not sampling configurations outside of the membrane (i.e. in water)? I would think that would solve your problem. You don't show any configurations in which the peptide is completely dissociated from the membrane. I don't know your objectives, but I would think that if you could completely extract the peptide from the membrane after passing through it, this would solve your problem. (2) In each window, I used the corresponding configuration that generated by the pulling simulation as initial input and run umbrella sampling. The size of each window is 0.15 nm, but close to the bilayer cneter (e.g., -0.6d0.6), I have increased number of windows so that the width of the window is to be 0.05 or 0.1 nm, I also tried to use different force constant in these windows. From the figure (http://www.flickr.com/photos/lijg/5467080971/) , we can classify the peptide conformation to be either extended (interacting with two bilayers) or compact (interacting with only one bilayer). Ideally, the peptide conformation should be similar for d=x and d=-x. The problem is that the configuration of peptide is not symmetric with respect to the bilayer center. For example, the peptide configuration is compact at d=0.6
[gmx-users] Can g_wham support using different temperature for different windows?
Dear all, I want to get the PMF of my peptide across the membrane bilayer. First I pulled my peptide across the membrane and then did windowed umbrella sampling along the reaction coordinates which is the z-distance between peptide and membrane. However, I found that sampling is not sufficient in some windows(e.g., around the center of the membrane). To enhance the sampling, I am thinking to run the simulation in those windows at higher temperature (e.g., 500K), but this will introduce a bias. My question is: can g_wham remove the bias due to using different temperatures in different windows? If g_wham cannot deal with the bias due to using different T, I may need to do REMD in those windows. But that will be very expensive computationally. Anybody have an idea of enhancing sampling in those windows? Btw, I am using Martini CG model. Any suggestions will be highly appreciated, thank you! Cheers, 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
Re: [gmx-users] Can g_wham support using different temperature for different windows?
Thanks for your comments, Justin. Using timestep of 20 fs, in each window the simulation runs for 100 ns CG time. The pulling rate is 0.001 nm/ps. Is it too fast? My system is a little different. My peptide is highly positively charged. The NMR experiments show that the conformation of the peptide in water is very dynamic, so I make it flexible without fixing any secondary structure in Martini model. In the membrane, 25% of the lipids are negatively charged, so there are very strong electrostatic attraction between peptides and membrane. During the peptide approaching the membrane from the top, peptide can take different configurations at different reaction coordinates. When pulling the peptide into the membrane, the peptide takes relatively compact structure and interacts with only the top leaflet until the distance becomes smaller than 0.45 nm, after that the peptide becomes extended structure and interacts with both leaflets. This extended structure remains until the distance becomes -1.05 nm. Further pulling leads to compact structure and interacts only with the lower leaflet. So the comformation of the peptide is not symmetric between the center of the bilayer, which leads to Hysteresis. It seems that there is a huge energy barrier for the peptide to translocate across the membrane because if the initial conformation in a certain window is extended (interacting with both leaflets), then it remains extended. Similarly, it the initial conformation in a certain window is compact (interacting with only one leaflet), it will remain compact. Any Suggestions of dealing with the highly charged system? Cheers, Jianguo From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Tuesday, 22 February 2011 09:58:36 Subject: Re: [gmx-users] Can g_wham support using different temperature for different windows? Jianguo Li wrote: Thanks Justin. I tried your suggestions by either increase more windows and change the force constant, but it seems the samplings are still bad in some windows. When I did pulling in (0 0 1) direction and a reverse pulling in (0 0 -1) direction, I got different configurations at certain reaction coordinates. And the windowed umbrella sampling seems depends strongly on the initial configurations in that window. Therefore I got different PMFs using pulling in (0 0 1) direction and reverse pulling in （0 0 -1) direction. How long are each of the simulations in each window? Sufficient sampling should eliminate any configurational bias and/or hysteresis. Also, if the pulling that sets up the initial configurations is done slowly enough, you won't see these problems. Sounds to me like you're pulling too fast or hard, such that the system is not stable. In my simulation, I exert constraints on phosphate atoms in z direction, so there is no lipid flip-flop and the membrane will be stable at high temperatures. Then I am thinking of increasing temperature in those bad windows to enhance sampling... I don't know if I can make a convincing argument here, but intuitively, these windows would be sampling in a different ensemble, so the free energy landscape in these windows would be discontinuous with any adjacent windows that are done at different temperatures, and perhaps the forces required to restrain your peptide at a given COM distance will still result in a discontinuous PMF. I would also suspect that g_wham can't handle this situation; it has a -temp flag, but it only takes one value. So if you construct your PMF curve using WHAM, but supply incorrect or inconsistent information, I certainly wouldn't believe the result. I guess the main point is, there are tons of published demonstrations of peptides and other molecules crossing a membrane with SMD and umbrella sampling, so it should be possible to generate stable configurations without any funny tricks. -Justin best regards, Jianguo *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Tuesday, 22 February 2011 09:35:37 *Subject:* Re: [gmx-users] Can g_wham support using different temperature for different windows? Jianguo Li wrote: Dear all, I want to get the PMF of my peptide across the membrane bilayer. First I pulled my peptide across the membrane and then did windowed umbrella sampling along the reaction coordinates which is the z-distance between peptide and membrane. However, I found that sampling is not sufficient in some windows(e.g., around the center of the membrane). To enhance the sampling, I am thinking to run the simulation in those windows at higher temperature (e.g., 500K), but this will introduce a bias. My question is: can g_wham remove the bias due to using different temperatures in different windows
Re: [gmx-users] Can g_wham support using different temperature for different windows?
Thanks Justin and Chris and sorry for confusing interpretation. Let me make it more clear. My peptide is flexible Martini beads, and highly positively charged. My membrane is a mixture of negatively charged lipids (25%) and zitterionic lipids(75%). So there is strong electrostatic attraction between peptide and membrane. To get the PMF, I did the following: (1) I did pulling simulation along (0 0 -1) direction to pull my peptide across the membrane. Then I got different configurations corresponding to different windows along the reaction coordinates, which is the z-distance between peptide and membrane. This figure (http://www.flickr.com/photos/lijg/5467080971/) shows some of the configurations at certain reaction coordinates. (2) In each window, I used the corresponding configuration that generated by the pulling simulation as initial input and run umbrella sampling. The size of each window is 0.15 nm, but close to the bilayer cneter (e.g., -0.6d0.6), I have increased number of windows so that the width of the window is to be 0.05 or 0.1 nm, I also tried to use different force constant in these windows. From the figure (http://www.flickr.com/photos/lijg/5467080971/) , we can classify the peptide conformation to be either extended (interacting with two bilayers) or compact (interacting with only one bilayer). Ideally, the peptide conformation should be similar for d=x and d=-x. The problem is that the configuration of peptide is not symmetric with respect to the bilayer center. For example, the peptide configuration is compact at d=0.6 and d=0.9, but the peptide is extended at d=-0.6 and d=-0.9. This leads Hysteresis. If I use g_wham to generate PMF, then the PMF is not symmetric with respect to the bilayer center. Using more number of windows and different force constant did not remove the problem. In my opinion, at least in some windows, the peptide should sample both compact and extended structure. But what I found is that the windowed umbrella simulation depends on the initial peptide conformation. If the initial peptide conformation is compact, then after 100 ns, it is still compact; if the initial peptide in that window is extended, the final configuration is also extended. I also tried to run longer equilibrium time (e.g., 200 ns), but the problem still exists. My question is how to increase sampling of the peptide conformation? I just think of two choices: (1) use high temperature (e.g., 500K) at those bad windows. As I mentioned, I am wondering if g_wham can unbias the effect of using different temperatures in different windows. (2) use REMD in those bad windows. These need a lot of computational resources. Is there any other method to deal with the insufficient sampling? Any suggestions are welcome, thanks for your time reading this email! Cheers, Jianguo From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Tuesday, 22 February 2011 11:13:05 Subject: Re: [gmx-users] Can g_wham support using different temperature for different windows? Jianguo Li wrote: Thanks for your comments, Justin. Using timestep of 20 fs, in each window the simulation runs for 100 ns CG time. The pulling rate is 0.001 nm/ps. Is it too fast? Let me clarify things, since I'm not convinced I understand your procedure. You generate a series of configurations with 0.001 nm/ps pulling, but then how many windows do you generate for independent simulations? What are your .mdp parameters during those windows? The pull rate should be 0 during the actual umbrella sampling, to restrain the peptide within the window. What force constant(s) do you use? My system is a little different. My peptide is highly positively charged. The NMR experiments show that the conformation of the peptide in water is very dynamic, so I make it flexible without fixing any secondary structure in Martini model. As was discussed in the last few days, do not interpret changes in structure too directly when using MARTINI. It is not designed to faithfully mimic secondary structure changes. In the membrane, 25% of the lipids are negatively charged, so there are very strong electrostatic attraction between peptides and membrane. During the peptide approaching the membrane from the top, peptide can take different configurations at different reaction coordinates. When pulling the peptide into the membrane, the peptide takes relatively compact structure and interacts with only the top leaflet until the distance becomes smaller than 0.45 nm, after that the peptide becomes extended structure and interacts with both leaflets. This extended structure remains until the distance becomes -1.05 nm. Further pulling leads to compact structure and interacts only with the lower leaflet. So the comformation of the peptide is not symmetric between the center of the bilayer, which leads to Hysteresis. It seems
Re: [gmx-users] Protein-membrane system
Hi, 3000 water molecule per lipids per second corresponds to 0.000384 water molecules transferred across the membrane per nano second (assume the system contains 128 lipids). It seems water translocation should not be observed in a simulation of 10 ns, but I am not sure. And I only find one reference paper(Biophysical Journal, Volume 96, 2009, pg4493–4501) about the water translocation across the membrane, in which a asymmetric membrane is used. I also have similar observations for my protein-membrane system. I observed 10~15 times water translocation arosss the membrane during 100 ns simulation when my protein adsorbed on the membrane. I am wondering these water translocation is normal in all-atom simulations or they are due to the protein-induced membrane deformation? Any comment is highly appreciated, thank you! best regards, Jianguo From: Itamar Kass itamar.k...@monash.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, 17 February 2011 07:20:19 Subject: Re: [gmx-users] Protein-membrane system Dear Aldo, It is totally OK to see water molecules within the bilayer, both in simulations and real life. If I am not totally wrong, 3000 water molecule per lipids per second are being transferred across the bilayer without any protein involvement. If your system is stable, the lipids density profile seems OK as well as its the thickness, you are fine. Cheers, Itamar. On 17/02/11 5:48 AM, Justin A. Lemkul wrote: Aldo Segura wrote: Dear gmx-users, I completed a MD (10 ns) of my protein-membrane system. When I perform a visual inspection (VMD) of md_0_1.gro file I observed a few water molecules within the bilayer. In previous steps (e.g. equilibration) this was not observed. Could be expected such behavior? Membrane protein systems take a long time (tens of ns or maybe more) to equilibrate, so some water may drift in and out during the initial few ns as voids in the lipids open and close. Nothing to worry about, unless for some reason they persist out past the expected equilibration time. -Justin Best regards, *//* */== = Aldo Segura-Cabrera Laboratorio de Bioinformática Centro de Biotecnología Genómica Instituto Politécnico Nacional Blvd. Del Maestro esquina Elías Piña, 88710 Reynosa, Tamaulipas, México. (899)9243627 ext. 87747 e-mail: asegu...@ipn.mx mailto:asegu...@ipn.mx; aldoseg...@gmail.com mailto:aldoseg...@gmail.com == ===/* -- In theory, there is no difference between theory and practice. But, in practice, there is. - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu -- 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] local pressure calcuation for Gromacs-4.5
Hi All, I found there is a customised version gromacs-4.0.2_localpressure for calculating the local pressure from the Gromacs website. I am wondering is there a higher version? The reason is that I am using CHARMM FF and have done membrane simulations using Gromacs-4.5. If I understand correctly, I need to rerun the simulation using the customized version of Gromacs to calculate the local pressure. However, I cannot use the -rerun option of gromacs-4.0.2_localpressure as my trajectory is from a higher version. Or is there any other tools that can calculate the local pressure of the membrane? Thanks very much! best regards, 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] box length in z dimension keep increasing when using two walls in NPT ensemble
Dear all, I was trying to add two walls at z=0 and z=z_box to my system which contains one peptide and one membrane. Since I am interested in how the peptides affect membrane properties (i.e., area per lipid), I need to use semi-isotropic pressure coupling. But I wanted to mimick the two-dimensional periodicity of the membrane and thus don't want to include the z-component of the ewald summation, so I decided to add two walls so that I can use ewald_geometry=3dc. Since there is no periodicity in z dimension, I kept two regions up and below the membrane neutral. However, when the simulation proceeds, the box length in z dimemsion keep increasing and results in a large vacum between image boxes in z dimension. Could anyone help me figure out what's going wrong? The following is my mdp file and I will be glad to provide any other details if needed: cpp = /usr/bin/cpp constraints = hbonds integrator = md dt = 0.002 ; ps ! nsteps = 1 ;. nstxout = 5 ; nstxtcout = 1000 nstvout = 0 nstfout = 0 nstlog = 100 nstenergy = 1000 nstlist = 5 ns_type = grid rlist = 1.2 coulombtype = PME rcoulomb = 1.2 rvdw = 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes Tcoupl = Nose-Hoover tc-grps = Protein lipid SOL_Ion tau_t = 0.5 0.5 0.5 ref_t = 310 310 310 ;Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = semiisotropic ; uniform scaling of x-y box vectors, independent z tau_p = 1.0 1.0 ; time constant, in ps ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, bar^-1 gen_vel = no gen_temp = 310.0 gen_seed = 173529 nstcomm = 5 comm-mode = Linear comm-grps = Protein_lipid SOL_Ion ; put two walls pbc = xy ewald_geometry = 3dc nwall = 2 wall_atomtype = C C wall_type = 12-6 wall_ewald_zfac = 3 wall_r_linpot = 0.5 Thanks very much! Cheers, Jianguo Postdoc, BIISERI, Singapore -- 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] questions about long-range electrostatic interaction in membrane systems
Dear All, I am working on the interaction of a positively charged peptide (18AA) and the bacterial membrane consisting of a mixture of zitterionic and negatively charged lipids. Our experiments show that the peptide can disrutp the membrane. One problem puzzed me is that which method to use in treating the long-range electrostatic interactions for my system. The following is my understanding, please correct me if I am wrong. There are two options for treating long-range electrostatic interactions for my system: (a) use a normal 3-D PME (by setting ewald_geometry=3d, which is the defaut option); and (b) use a slab PME in 2-D by setting ewald_geometry=3dc (thanks for David Bostick's suggestions) If I use normal PME in 3-D (ewald_geometry=3d), and put the peptide on top of the membrane, I cannot increase the peptide concentration. For example, if I put 3 peptide on top of the membrane, 1 peptide will move to the lower leaflet of top image box. I believe this is because of the repulsion between the peptide and also the attraction between the peptide and the lower leaflet of the membrane in the top image box. Also as mentioned in the previous posts, 3D PME has artifact (i.e., due to the dipole moment of the simulation box which is significant as pointed out by David Bostick through emails since I have a positively charged peptide and a negatively charged membrane). When using 2D PME with slab geometry (ewald_geometry=3dc), the membrane is treated as an infinite charged slab, the positively charged peptide is not only interacts with the membrane in the central box, but also interacts with the membrane in the image boxes. Although the interaction between the peptide and the membrane in the image boxes far from the central box is very weak, but the overal sum of all these interactions could be very strong since there are infinite number of image boxes. Therefore it will over-estimate the intearction betwen the peptide and the membrane. In fact, I got very different results when setting ewald_geometry being 3d or 3dc. Using ewald_geometry=3d, nothing happens except a minor deformation of the membrane in the vicinity of the peptide. However, when using ewald_geometry=3dc, the peptide readily induce a water pore and penetrate into the membrane. I am not sure if the results using 2d PME is correct or not, as it has some artifact for my system. I am wondering how big the artifact is due to the infinity of the 2D PME for slab geometry. Any suggestions for modeling the finite size of the cell membrane are appreciated! Another question is about the parameter epsilong_surface in Gromacs which is the dipole correction of Ewald summation. Is it suitable to use this parameter in my simulations? If possible, which value I need to use for this parameter? Sorry for so many questions, thanks for your time! best regards, Jianguo Postdoc Research Fellow Bioinformatics Institute and Singapore Eye Research Institute, Singapore -- 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
