[gmx-users] Does Gromacs support CHARMM force field now?
Hi all GMX users: I noticed that there're charmm27 force field files in Gromacs-4.0.5 software package. But charmm27 force field can't be choosed in pdb2gmx. So can I use charmm27 force field in Gromacs now? Thanks for any advice in advance! 2009-11-11 Ji Xu The State Key Laboratory of Multiphase Complex System Institute of Process Engineering Chinese Academy of Sciences Beijing 100190, China Tel.: +86 10 8262 3713-804 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] solvation energy calculation
Hi all, I am trying to repeat the solvation energy calculation as done by Villa and MArk in (A. Villa and A. E. Mark Calculation of the free energy of solvation for neutral analogues of amino acid side chains. J. Comput. Chem, 23 (2002) 548-553.). I am not sure about the way I am doing my in vacuum simulation. attached is my mdp: integrator = sd . . . ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = berendsen ; Groups to couple separately, time constant (ps) and reference temperature (K) tc-grps = system tau-t = 0.1 ref-t = 298 ; Pressure coupling Pcoupl = no ; Generate velocites is on at 290K - do not get velocity from gro file. gen_vel = yes gen_temp = 290 ld_seed = 12 ; Free energy control stuff free-energy = yes init-lambda = 0 ; Topology A (lambda=0) to topology B (lambda=1). delta-lambda = 0 sc-alpha = 0.5 ; soft core potantial sc-power = 1 sc-sigma = 0.3 . . . ; Center of mass control nstcomm = 1 ; Periodic boundary conditions pbc = xyz comm_mode = angular My question are: 1. Is there any meaning or temperature when one does SD in vacuum? 2. Does my lambda parameters ore fine? 3. Does the way I treat the center of mass motions is OK? Best, Itamar --- "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...@med.monash.edu.au -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to generate xvg files
On Tue, Nov 10, 2009 at 7:02 PM, Jack Shultz wrote: > I'm trying to get the xtc output. The mdp file has these parameters. > Is the nstxtcout what specifiies it to generate xtc? > yes its the freq of writing co - ordinates > nsteps = 2000 ; Maximum number of (minimization) > steps to perform > nstenergy = 10; Write energies to disk every nstenergy > steps > nstxtcout = 10; Write coordinates to disk every > nstxtcout steps > > Do I need to use this -x flag? > mdrun -nice 0 -s em.tpr -x > No xtc was created though > -x is for writing xtc file http://manual.gromacs.org/current/online/mdrun.html should help > > On Tue, Nov 10, 2009 at 9:43 PM, Amit Choubey wrote: > > > > > > On Tue, Nov 10, 2009 at 6:31 PM, Jack Shultz > > > wrote: > >> > >> Actually I guess I need to generate the xtc first before I can get the > xvg > >> > >> I am trying to develop a workflow for this > >> mdrun > >> g dist calculates the distances between the centers of mass of two > groups > >> g bond calculates distances between atoms > >> g msd calculates mean square displacements > >> g rms calculates rmsd’s with a reference structure and rmsd matrices > >> g rmsf calculates atomic fluctuations > >> g energy writes energies to xvg files and displays averages > > > > Thats true. First you need to do the simulation 'mdrun' and then analyze > the > > trajectory (.xtc) and energy (.edr) files generated. It takes quite some > > time to figure out the first step 'mdrun' :) > > amit > > > > > >> > >> On Tue, Nov 10, 2009 at 9:24 PM, Amit Choubey > wrote: > >> > > >> > > >> > On Tue, Nov 10, 2009 at 6:11 PM, Jack Shultz > >> > > >> > wrote: > >> >> > >> >> Hi I am trying to generate xvg files for my simulation. Which > >> >> parameter do I need to specify? > >> > > >> > xvg files for what? They are used for data files for 2D plots of > >> > quantities > >> > that can be analyzed... > >> > Can you be more specific? > >> > amit > >> >> > >> >> -- > >> >> Jack > >> >> > >> >> http://drugdiscoveryathome.com > >> >> http://hydrogenathome.org > >> >> -- > >> >> gmx-users mailing listgmx-users@gromacs.org > >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> >> Please search the archive at http://www.gromacs.org/search before > >> >> posting! > >> >> Please don't post (un)subscribe requests to the list. Use the > >> >> www interface or send it to gmx-users-requ...@gromacs.org. > >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >> > > >> > > >> > -- > >> > gmx-users mailing listgmx-users@gromacs.org > >> > http://lists.gromacs.org/mailman/listinfo/gmx-users > >> > Please search the archive at http://www.gromacs.org/search before > >> > posting! > >> > Please don't post (un)subscribe requests to the list. Use the > >> > www interface or send it to gmx-users-requ...@gromacs.org. > >> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >> > > >> > >> > >> > >> -- > >> Jack > >> > >> http://drugdiscoveryathome.com > >> http://hydrogenathome.org > >> -- > >> gmx-users mailing listgmx-users@gromacs.org > >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> Please search the archive at http://www.gromacs.org/search before > posting! > >> Please don't post (un)subscribe requests to the list. Use the > >> www interface or send it to gmx-users-requ...@gromacs.org. > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > -- > Jack > > http://drugdiscoveryathome.com > http://hydrogenathome.org > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to generate xvg files
Jack Shultz wrote: I'm trying to get the xtc output. The mdp file has these parameters. Is the nstxtcout what specifiies it to generate xtc? nsteps = 2000 ; Maximum number of (minimization) steps to perform nstenergy = 10; Write energies to disk every nstenergy steps nstxtcout = 10; Write coordinates to disk every nstxtcout steps Probably. See manual section 7.3.8 Do I need to use this -x flag? mdrun -nice 0 -s em.tpr -x No xtc was created though -x is not a flag - it accepts a filename / filename prefix. Omitting it entirely will probably generate traj.xtc. Experiment and see. Mark On Tue, Nov 10, 2009 at 9:43 PM, Amit Choubey wrote: On Tue, Nov 10, 2009 at 6:31 PM, Jack Shultz wrote: Actually I guess I need to generate the xtc first before I can get the xvg I am trying to develop a workflow for this mdrun g dist calculates the distances between the centers of mass of two groups g bond calculates distances between atoms g msd calculates mean square displacements g rms calculates rmsd’s with a reference structure and rmsd matrices g rmsf calculates atomic fluctuations g energy writes energies to xvg files and displays averages Thats true. First you need to do the simulation 'mdrun' and then analyze the trajectory (.xtc) and energy (.edr) files generated. It takes quite some time to figure out the first step 'mdrun' :) amit On Tue, Nov 10, 2009 at 9:24 PM, Amit Choubey wrote: On Tue, Nov 10, 2009 at 6:11 PM, Jack Shultz wrote: Hi I am trying to generate xvg files for my simulation. Which parameter do I need to specify? xvg files for what? They are used for data files for 2D plots of quantities that can be analyzed... Can you be more specific? amit -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] doing exact continuation
Amit Choubey wrote: Hi everyone, I want to do an exact continuation with saved configuration and velocity. What are the options that i need to change in mdp file? I know i have to make unconstrained_start = yes. Anything else? The reason i am asking this is that it is kind of difficult to make sure if i am doing the right thing by comparing two different trajectories. This is because the trajectories are generally 'chaotic' and they diverge even if there is a difference in the numbers due to the machine. So i want to do the best from my part. The details vary with GROMACS version and what you're actually trying to do. See http://www.gromacs.org/Documentation/How-tos/Doing_Restarts and http://www.gromacs.org/Documentation/How-tos/Extending_Simulations Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to generate xvg files
I'm trying to get the xtc output. The mdp file has these parameters. Is the nstxtcout what specifiies it to generate xtc? nsteps = 2000 ; Maximum number of (minimization) steps to perform nstenergy = 10; Write energies to disk every nstenergy steps nstxtcout = 10; Write coordinates to disk every nstxtcout steps Do I need to use this -x flag? mdrun -nice 0 -s em.tpr -x No xtc was created though On Tue, Nov 10, 2009 at 9:43 PM, Amit Choubey wrote: > > > On Tue, Nov 10, 2009 at 6:31 PM, Jack Shultz > wrote: >> >> Actually I guess I need to generate the xtc first before I can get the xvg >> >> I am trying to develop a workflow for this >> mdrun >> g dist calculates the distances between the centers of mass of two groups >> g bond calculates distances between atoms >> g msd calculates mean square displacements >> g rms calculates rmsd’s with a reference structure and rmsd matrices >> g rmsf calculates atomic fluctuations >> g energy writes energies to xvg files and displays averages > > Thats true. First you need to do the simulation 'mdrun' and then analyze the > trajectory (.xtc) and energy (.edr) files generated. It takes quite some > time to figure out the first step 'mdrun' :) > amit > > >> >> On Tue, Nov 10, 2009 at 9:24 PM, Amit Choubey wrote: >> > >> > >> > On Tue, Nov 10, 2009 at 6:11 PM, Jack Shultz >> > >> > wrote: >> >> >> >> Hi I am trying to generate xvg files for my simulation. Which >> >> parameter do I need to specify? >> > >> > xvg files for what? They are used for data files for 2D plots of >> > quantities >> > that can be analyzed... >> > Can you be more specific? >> > amit >> >> >> >> -- >> >> Jack >> >> >> >> http://drugdiscoveryathome.com >> >> http://hydrogenathome.org >> >> -- >> >> gmx-users mailing list gmx-us...@gromacs.org >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> >> Please search the archive at http://www.gromacs.org/search before >> >> posting! >> >> Please don't post (un)subscribe requests to the list. Use the >> >> www interface or send it to gmx-users-requ...@gromacs.org. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > >> > >> > -- >> > gmx-users mailing list gmx-us...@gromacs.org >> > http://lists.gromacs.org/mailman/listinfo/gmx-users >> > Please search the archive at http://www.gromacs.org/search before >> > posting! >> > Please don't post (un)subscribe requests to the list. Use the >> > www interface or send it to gmx-users-requ...@gromacs.org. >> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > >> >> >> >> -- >> Jack >> >> http://drugdiscoveryathome.com >> http://hydrogenathome.org >> -- >> gmx-users mailing list gmx-us...@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to generate xvg files
Jack Shultz wrote: Hi I am trying to generate xvg files for my simulation. Which parameter do I need to specify? An .xvg file is the output of an analysis tool, suitable for plotting using xmgrace, not some specific output of, i.e. mdrun. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to generate xvg files
On Tue, Nov 10, 2009 at 6:31 PM, Jack Shultz wrote: > Actually I guess I need to generate the xtc first before I can get the xvg > > I am trying to develop a workflow for this > mdrun > g dist calculates the distances between the centers of mass of two groups > g bond calculates distances between atoms > g msd calculates mean square displacements > g rms calculates rmsd’s with a reference structure and rmsd matrices > g rmsf calculates atomic fluctuations > g energy writes energies to xvg files and displays averages > Thats true. First you need to do the simulation 'mdrun' and then analyze the trajectory (.xtc) and energy (.edr) files generated. It takes quite some time to figure out the first step 'mdrun' :) amit > > On Tue, Nov 10, 2009 at 9:24 PM, Amit Choubey wrote: > > > > > > On Tue, Nov 10, 2009 at 6:11 PM, Jack Shultz > > > wrote: > >> > >> Hi I am trying to generate xvg files for my simulation. Which > >> parameter do I need to specify? > > > > xvg files for what? They are used for data files for 2D plots of > quantities > > that can be analyzed... > > Can you be more specific? > > amit > >> > >> -- > >> Jack > >> > >> http://drugdiscoveryathome.com > >> http://hydrogenathome.org > >> -- > >> gmx-users mailing listgmx-users@gromacs.org > >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> Please search the archive at http://www.gromacs.org/search before > posting! > >> Please don't post (un)subscribe requests to the list. Use the > >> www interface or send it to gmx-users-requ...@gromacs.org. > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > -- > Jack > > http://drugdiscoveryathome.com > http://hydrogenathome.org > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to generate xvg files
Actually I guess I need to generate the xtc first before I can get the xvg I am trying to develop a workflow for this mdrun g dist calculates the distances between the centers of mass of two groups g bond calculates distances between atoms g msd calculates mean square displacements g rms calculates rmsd’s with a reference structure and rmsd matrices g rmsf calculates atomic fluctuations g energy writes energies to xvg files and displays averages On Tue, Nov 10, 2009 at 9:24 PM, Amit Choubey wrote: > > > On Tue, Nov 10, 2009 at 6:11 PM, Jack Shultz > wrote: >> >> Hi I am trying to generate xvg files for my simulation. Which >> parameter do I need to specify? > > xvg files for what? They are used for data files for 2D plots of quantities > that can be analyzed... > Can you be more specific? > amit >> >> -- >> Jack >> >> http://drugdiscoveryathome.com >> http://hydrogenathome.org >> -- >> gmx-users mailing list gmx-us...@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to generate xvg files
On Tue, Nov 10, 2009 at 6:11 PM, Jack Shultz wrote: > Hi I am trying to generate xvg files for my simulation. Which > parameter do I need to specify? > xvg files for what? They are used for data files for 2D plots of quantities that can be analyzed... Can you be more specific? amit > > -- > Jack > > http://drugdiscoveryathome.com > http://hydrogenathome.org > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to generate xvg files
Hi I am trying to generate xvg files for my simulation. Which parameter do I need to specify? -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] doing exact continuation
Hi everyone, I want to do an exact continuation with saved configuration and velocity. What are the options that i need to change in mdp file? I know i have to make unconstrained_start = yes. Anything else? The reason i am asking this is that it is kind of difficult to make sure if i am doing the right thing by comparing two different trajectories. This is because the trajectories are generally 'chaotic' and they diverge even if there is a difference in the numbers due to the machine. So i want to do the best from my part. thank you, Amit -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Increase temperature to 550K
I agree with Mark's earlier comment; the water model alone is not the most immediate concern. A colleague of mine is currently doing lots of high-temperature (up to 600 K) simulations of proteins in TIP3P using the AMBER force fields. There are plenty of other methodological concerns (pressure coupling especially); a thorough search of the literature will give you some insights into what might be wrong. Plenty of groups have successfully been doing high-temperature MD for a number of years. -Justin Chih-Ying Lin wrote: Hi the water model is TIP3P. Thanks Lin I think the problem is hidden in your water force field model. > The simulation system is merely water + one lysozyme. > I increase temperate to 550K. > > Then, the simulation broke. > The following message is shown. > > MX:hpc0011:Remote endpoint is closed, peer=00:60:dd:48:14:5b (hpc0010:0) > mpiexec: Warning: task 0 exited with status 1. > mpiexec: Warning: tasks 1-2 died with signal 9 (Killed). > mpiexec: Warning: task 3 died with signal 11 (Segmentation fault). > > > Anything wrong with the simulation? > > Thank you -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Increase temperature to 550K
Hi the water model is TIP3P. Thanks Lin I think the problem is hidden in your water force field model. > The simulation system is merely water + one lysozyme. > I increase temperate to 550K. > > Then, the simulation broke. > The following message is shown. > > MX:hpc0011:Remote endpoint is closed, peer=00:60:dd:48:14:5b (hpc0010:0) > mpiexec: Warning: task 0 exited with status 1. > mpiexec: Warning: tasks 1-2 died with signal 9 (Killed). > mpiexec: Warning: task 3 died with signal 11 (Segmentation fault). > > > Anything wrong with the simulation? > > Thank you -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Increase temperature to 550K
> Vitaly V. Chaban wrote: >> I think the problem is hidden in your water force field model. > > On what basis? The user hasn't provided any information to suggest it's > other than a poorly-conditioned integration. On the basis of intuition. Most of the known water models behave incorrectly at such high temperatures. Be sure I guessed. :) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Charge group moving too much
Jennifer Williams wrote: Hello, One of my simulations just crashed after 660,000 steps with the following message: Step 660560: The charge group starting at atom 4100 moved than the distance allowed by the domain decomposition (1.50) in direction X distance out of cell 2.356293 Old coordinates:1.7520.4470.751 New coordinates:3.5931.5320.674 Old cell boundaries in direction X:0.0002.116 New cell boundaries in direction X:0.0002.122 --- Program mdrun, VERSION 4.0.5 Source code file: domdec.c, line: 3651 Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated --- "Why Weren't You at My Funeral ?" (G. Groenhof) Error on node 0, will try to stop all the nodes Halting parallel program mdrun on CPU 0 out of 8 I am modelling flexible alkyl chains which are anchored to a frozen silica wall. This particular atom (4100) is at the edge of the periodic boundary condition so I am guessing that what happens is that while the anchored side stays where it is, the other free end wanders into the next cell and this perhaps triggers the error message? If this is indeed the problem, is there some way to stop the program stopping with an error message when this happens? The old and new coordinates reported aren't consistent with that, and the error message isn't "this bond is too long", it's "this group of atoms moved way too much last integration". I did do an energy minimisation before starting and my structure looks OK. It seems strange that it would crash only after 66 steps. Indeed. Also what is meant by the following? I am using NVT so my simulation cell should not change. Old cell boundaries in direction X:0.0002.116 New cell boundaries in direction X:0.0002.122 My cell is about 4.3 x 4.3 x 7.5 nm I am using gromacs-4.0.5 I'm mystified, but I know little about interactions with frozen groups. I don't think Vitaly's suggestion will help in the context of a simulation that runs for hundreds of thousands of steps. Whether or not you can reproduce the crash will be useful data. If so, construct a run that will stop just before it, and then continue on to the crash with nstxout = 1 so you can see whether these atoms are really moving lots, or perhaps a bug was provoked. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Increase temperature to 550K
Vitaly V. Chaban wrote: I think the problem is hidden in your water force field model. On what basis? The user hasn't provided any information to suggest it's other than a poorly-conditioned integration. Mark The simulation system is merely water + one lysozyme. I increase temperate to 550K. Then, the simulation broke. The following message is shown. MX:hpc0011:Remote endpoint is closed, peer=00:60:dd:48:14:5b (hpc0010:0) mpiexec: Warning: task 0 exited with status 1. mpiexec: Warning: tasks 1-2 died with signal 9 (Killed). mpiexec: Warning: task 3 died with signal 11 (Segmentation fault). Anything wrong with the simulation? Thank you -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Increase temperature to 550K
I think the problem is hidden in your water force field model. > The simulation system is merely water + one lysozyme. > I increase temperate to 550K. > > Then, the simulation broke. > The following message is shown. > > MX:hpc0011:Remote endpoint is closed, peer=00:60:dd:48:14:5b (hpc0010:0) > mpiexec: Warning: task 0 exited with status 1. > mpiexec: Warning: tasks 1-2 died with signal 9 (Killed). > mpiexec: Warning: task 3 died with signal 11 (Segmentation fault). > > > Anything wrong with the simulation? > > Thank you -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Charge group moving too much
Hi, The easiest way to fix the problem is to decrease the current timestep. Also please read about -dd and -rdd keys of mdrun utility. Vitaly > One of my simulations just crashed after 660,000 steps with the > following message: > > Step 660560: > The charge group starting at atom 4100 moved than the distance allowed > by the domain decomposition (1.50) in direction X > distance out of cell 2.356293 > Old coordinates: 1.752 0.447 0.751 > New coordinates: 3.593 1.532 0.674 > Old cell boundaries in direction X: 0.000 2.116 > New cell boundaries in direction X: 0.000 2.122 > > --- > Program mdrun, VERSION 4.0.5 > Source code file: domdec.c, line: 3651 > > Fatal error: > A charge group moved too far between two domain decomposition steps > This usually means that your system is not well equilibrated > --- > > "Why Weren't You at My Funeral ?" (G. Groenhof) > > Error on node 0, will try to stop all the nodes > Halting parallel program mdrun on CPU 0 out of 8 > > I am modelling flexible alkyl chains which are anchored to a frozen > silica wall. This particular atom (4100) is at the edge of the > periodic boundary condition so I am guessing that what happens is that > while the anchored side stays where it is, the other free end wanders > into the next cell and this perhaps triggers the error message? If > this is indeed the problem, is there some way to stop the program > stopping with an error message when this happens? > > I did do an energy minimisation before starting and my structure looks > OK. It seems strange that it would crash only after 66 steps. > > Also what is meant by the following? I am using NVT so my simulation > cell should not change. > > Old cell boundaries in direction X: 0.000 2.116 > New cell boundaries in direction X: 0.000 2.122 > > > My cell is about 4.3 x 4.3 x 7.5 nm > I am using gromacs-4.0.5 > > Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Walls In Gromacs
On Tue, Nov 10, 2009 at 4:32 AM, Marcovitz Amir wrote: > Hi Amit, > > Unfortunately, i don't have an answer to your question as i am a very > new GROMACS user myself.. > Actually i might need your help. > > I need to model two charged plates with opposite signs which are > solvated in an electrolyte solution. You might try to start with a boundary condition on the potential say something like constant potential on the plates. And then you can always find the electrostatic Green's function that solves the poisson's equation. >From there you could derive an expression for the potential in the box if the charge density were provided. This part is discussed in Classic Electrodynamics book by Jackson. Have a look at it if you need reference. You can use the above green's function for finding potential everywhere in box depending on the location of ions in the solution. The force due to this can then be implemented in MD. I am not very sure about the implementation though. > When I was desperately browsing for > keywords such as: Gromacs plates, walls, etc., trying to find the > slightest clue of how to approach this issue in gromacs i saw your > posting from the October 19th. > > I will most appreciate if you can give me some hint or tip of how to > approach this problem or what is the suitable chapter in the manual to > search for it. > I am not sure about any discussion on the specific type of things you are talking about. Wall function for MD simulation is disscussed in chapter 7. You will only find what options can be used. I think a tabulated function can also be used. > Sorry i couldn't help you with your question, hopefully you already > figured it out, > I think it beneficial for both of us to keep these discussion in the forum for our and other's benefit . Amit > > Regards, > Amir Marcovitz, > Weizmann Inst. of Science , Rehovot, Israel > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Increase temperature to 550K
Chih-Ying Lin wrote: Hi Here is the dt and constraints. Any other suggestion about heating up the system and make the system stable? Like anything else, thorough equilibration under the desired conditions. -Justin Thank you Lin dt = 0.001 ; OPTIONS FOR BONDS constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = yes lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 Chih-Ying Lin wrote: HI The simulation system is merely water + one lysozyme. I increase temperate to 550K. Then, the simulation broke. The following message is shown. MX:hpc0011:Remote endpoint is closed, peer=00:60:dd:48:14:5b (hpc0010:0) mpiexec: Warning: task 0 exited with status 1. mpiexec: Warning: tasks 1-2 died with signal 9 (Killed). mpiexec: Warning: task 3 died with signal 11 (Segmentation fault). Anything wrong with the simulation? I think, pretty clearly, yes. Increasing to a high temperature can make the system unstable. Are you using a suitable dt? Constraints? -Justin Thank you Lin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Increase temperature to 550K
Hi Here is the dt and constraints. Any other suggestion about heating up the system and make the system stable? Thank you Lin dt = 0.001 ; OPTIONS FOR BONDS constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = yes lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 Chih-Ying Lin wrote: > HI > The simulation system is merely water + one lysozyme. > I increase temperate to 550K. > > Then, the simulation broke. > The following message is shown. > > MX:hpc0011:Remote endpoint is closed, peer=00:60:dd:48:14:5b (hpc0010:0) > mpiexec: Warning: task 0 exited with status 1. > mpiexec: Warning: tasks 1-2 died with signal 9 (Killed). > mpiexec: Warning: task 3 died with signal 11 (Segmentation fault). > > > Anything wrong with the simulation? > I think, pretty clearly, yes. Increasing to a high temperature can make the system unstable. Are you using a suitable dt? Constraints? -Justin > Thank you > Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Remove solvent from results
Jack Shultz wrote: I guess it can be done with sed but is there another way using one of the Gromacs apps? Use trjconv, with a special index group that defines all non-solvent atoms (or whatever subset you want to save). You can also do this ahead of time by setting the appropriate xtc_grps in the .mdp file. -Justin On Tue, Nov 10, 2009 at 12:48 PM, Jack Shultz wrote: Hi Guys, I was wondering if there is any way to remove the solvent from your final trajectory results in mdrun? -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Remove solvent from results
I guess it can be done with sed but is there another way using one of the Gromacs apps? On Tue, Nov 10, 2009 at 12:48 PM, Jack Shultz wrote: > Hi Guys, > > I was wondering if there is any way to remove the solvent from your > final trajectory results in mdrun? > > -- > Jack > > http://drugdiscoveryathome.com > http://hydrogenathome.org > -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Remove solvent from results
Hi Guys, I was wondering if there is any way to remove the solvent from your final trajectory results in mdrun? -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Charge group moving too much
Hello, One of my simulations just crashed after 660,000 steps with the following message: Step 660560: The charge group starting at atom 4100 moved than the distance allowed by the domain decomposition (1.50) in direction X distance out of cell 2.356293 Old coordinates:1.7520.4470.751 New coordinates:3.5931.5320.674 Old cell boundaries in direction X:0.0002.116 New cell boundaries in direction X:0.0002.122 --- Program mdrun, VERSION 4.0.5 Source code file: domdec.c, line: 3651 Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated --- "Why Weren't You at My Funeral ?" (G. Groenhof) Error on node 0, will try to stop all the nodes Halting parallel program mdrun on CPU 0 out of 8 I am modelling flexible alkyl chains which are anchored to a frozen silica wall. This particular atom (4100) is at the edge of the periodic boundary condition so I am guessing that what happens is that while the anchored side stays where it is, the other free end wanders into the next cell and this perhaps triggers the error message? If this is indeed the problem, is there some way to stop the program stopping with an error message when this happens? I did do an energy minimisation before starting and my structure looks OK. It seems strange that it would crash only after 66 steps. Also what is meant by the following? I am using NVT so my simulation cell should not change. Old cell boundaries in direction X:0.0002.116 New cell boundaries in direction X:0.0002.122 My cell is about 4.3 x 4.3 x 7.5 nm I am using gromacs-4.0.5 Thanks -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_sdf gives wrong refmol with multiple center molecules
Hi, just for reference, I have filed a bug report on this (and one other issue with g_sdf): http://bugzilla.gromacs.org/show_bug.cgi?id=356 Best, Ondrej On Tue, Nov 10, 2009 at 16:35, Rasmus "Termo" Lundsgaard wrote: > Hi Atte > > Did you find a solution to this problem?? I'm doing the same calculations as > you describe, and wanted to try it out on TIP4p water first - which gives > the wrong coordinates for the ref molecule by the -r flag as you > described?!? > > The distribution looks completely right though... > > Anyone got an idea of where it goes wrong and how the .gro can be translated > easily to the right center place?? > > I have also tried using the g_spatial function. but here my problems stops > on of how to make the xtc file with trjconv in a easy way so it will have > each water molecule as the center molecule and a big xtc file. Right now I > can do it for all time frames with one designated water molecule. this will > only give me the distribution function around one water molecule - instead > of using all of them... I would like all time frames for 1st water molecule, > then all time frames for 2nd water molecules, etc. in one xtc file... > > Best regards > Rasmus > > >> Hi, >> >> if you give g_sdf just one molecule (in mode 1) to look at the >> distribution of other atoms around it, everything looks fine. However, if >> you give two or more molecules, the refmol.gro that is printed is messed up, >> but the actual density map still looks ok. You can try this with the 216 >> water molecule tutorial case. >> >> Run a short md writing frames into traj.xtc. >> Append these lines to the index.ndx (which has only OW group before >> these). >> [ O1 ] >> 1 4 >> [ H1 ] >> 2 5 >> [ H2 ] >> 3 6 >> >> or >> [ O1 ] >> 1 >> [ H1 ] >> 2 >> [ H2 ] >> 3 >> >> give >> g_sdf -s topol.tpr -f traj.xtc -n index.ndx -r >> 2 >> 3 >> 4 >> 1 >> and have a look at the refmol.gro in the two cases. >> >> Is there something wrong in adding up the coordinates? >> >> Cheers, >> Atte >> >> > > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Dummy masses for the Amber FF
Dear all, I have noticed that the .ddb file are not present in the port of the Amber FF available at http://chemistry.csulb.edu/ffamber/. Does anyone know if they are perhaps available elsewhere or if something has been done in this direction? Thanks for any information, Ondrej Marsalek -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_sdf gives wrong refmol with multiple center molecules
Hi Atte Did you find a solution to this problem?? I'm doing the same calculations as you describe, and wanted to try it out on TIP4p water first - which gives the wrong coordinates for the ref molecule by the -r flag as you described?!? The distribution looks completely right though... Anyone got an idea of where it goes wrong and how the .gro can be translated easily to the right center place?? I have also tried using the g_spatial function. but here my problems stops on of how to make the xtc file with trjconv in a easy way so it will have each water molecule as the center molecule and a big xtc file. Right now I can do it for all time frames with one designated water molecule. this will only give me the distribution function around one water molecule - instead of using all of them... I would like all time frames for 1st water molecule, then all time frames for 2nd water molecules, etc. in one xtc file... Best regards Rasmus Hi, if you give g_sdf just one molecule (in mode 1) to look at the distribution of other atoms around it, everything looks fine. However, if you give two or more molecules, the refmol.gro that is printed is messed up, but the actual density map still looks ok. You can try this with the 216 water molecule tutorial case. Run a short md writing frames into traj.xtc. Append these lines to the index.ndx (which has only OW group before these). [ O1 ] 1 4 [ H1 ] 2 5 [ H2 ] 3 6 or [ O1 ] 1 [ H1 ] 2 [ H2 ] 3 give g_sdf -s topol.tpr -f traj.xtc -n index.ndx -r 2 3 4 1 and have a look at the refmol.gro in the two cases. Is there something wrong in adding up the coordinates? Cheers, Atte -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Increase temperature to 550K
Chih-Ying Lin wrote: HI The simulation system is merely water + one lysozyme. I increase temperate to 550K. Then, the simulation broke. The following message is shown. MX:hpc0011:Remote endpoint is closed, peer=00:60:dd:48:14:5b (hpc0010:0) mpiexec: Warning: task 0 exited with status 1. mpiexec: Warning: tasks 1-2 died with signal 9 (Killed). mpiexec: Warning: task 3 died with signal 11 (Segmentation fault). Anything wrong with the simulation? I think, pretty clearly, yes. Increasing to a high temperature can make the system unstable. Are you using a suitable dt? Constraints? -Justin Thank you Lin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Increase temperature to 550K
HI The simulation system is merely water + one lysozyme. I increase temperate to 550K. Then, the simulation broke. The following message is shown. MX:hpc0011:Remote endpoint is closed, peer=00:60:dd:48:14:5b (hpc0010:0) mpiexec: Warning: task 0 exited with status 1. mpiexec: Warning: tasks 1-2 died with signal 9 (Killed). mpiexec: Warning: task 3 died with signal 11 (Segmentation fault). Anything wrong with the simulation? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Truncation of file traj.trr failed
ram bio wrote: Dear justin, The job was terminated as under: vol 0.92 imb F 1% step 5860300, will finish Sun Nov 15 06:56:32 2009 =>> PBS: job killed: walltime 86438 exceeded limit 86400 mpiexec: killing job... i think due to queueing system and maximum time being 24hrs. i donot know how to know whether new cpt files are written all the files i have are the same 2 cpt files state.cpt and state_prev.cpt. You will only ever have state.cpt and state_prev.cpt, but the timestamp on the file might give you a clue as to when they were written :) when i did gmxcheck on both cpt files the output was Checking file state.cpt # Atoms 31609 Last frame -1 time 2928.000 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 for state_prev.cpt # Atoms 31609 Last frame -1 time 2896.000 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 when the run is extended for the second time do gromacs generate a new cpt file i mean with new name or same named files (state.cpt and state_prev.cpt) with new check points written.. New checkpoint files are written every -cpt minutes (by default, 15). It looks like your simulation did not continue past 2928 ps, so do check the timestamp on all of your output files in case something weird is going on. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Truncation of file traj.trr failed
Dear justin, The job was terminated as under: vol 0.92 imb F 1% step 5860300, will finish Sun Nov 15 06:56:32 2009 =>> PBS: job killed: walltime 86438 exceeded limit 86400 mpiexec: killing job... i think due to queueing system and maximum time being 24hrs. i donot know how to know whether new cpt files are written all the files i have are the same 2 cpt files state.cpt and state_prev.cpt. when i did gmxcheck on both cpt files the output was Checking file state.cpt # Atoms 31609 Last frame -1 time 2928.000 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 for state_prev.cpt # Atoms 31609 Last frame -1 time 2896.000 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 when the run is extended for the second time do gromacs generate a new cpt file i mean with new name or same named files (state.cpt and state_prev.cpt) with new check points written.. Please help Thanks, Ram On Tue, Nov 10, 2009 at 7:02 PM, Justin A. Lemkul wrote: > > > ram bio wrote: >> >> Dear Justin, >> >> As per the suggestions in the bug, i changed the line in >> src/gmxlib/checkpoint.c file on the cluster: >> >> from >> outputfiles[i].offset = ( ((off_t) offset_high) << 32 )| ( (off_t) >> offset_low ); >> >> to >> outputfiles[i].offset = ( ((off_t) offset_high) << 32 )| ( (off_t) >> offset_low & mask ); >> >> and was able to use the -append option, my command was >> mpiexec -np 4 /usr/local/gromacs/bin/mdrun -v -g $myjob.log -s >> md20.tpr -cpi state.cpt -append >> >> and this run generated another 3ns production data (from the step >> 2928600 - 590) and thus increasing the size of trr file to 4.8 GB >> from 2.1 GB, because my simulation is for 20ns, i submitted one more >> job with the same command after completing the 5.9 ns, >> > > So the job crashed again, then? > >> mpiexec -np 4 /usr/local/gromacs/bin/mdrun -v -g $myjob.log -s >> md20.tpr -cpi state.cpt -append >> >> now again the job is starting from same step 2928600, i also tried >> using the command >> >> mpiexec -np 4 /usr/local/gromacs/bin/mdrun -v -g $myjob.log -s >> md20.tpr -cpi state_prev.cpt >> >> -append >> >> here also the output is same that is starting from 2928600 step, >> >> i want to continue the run from 590 step, please let me know how >> to proceed, do i have to generate a new .tpr file (my mdp file is >> defined for 20 ns and the output is md20.tpr) or can i use the same >> tpr file (md20.tpr) or i require to change the command to continue.. >> > > Were new .cpt files actually written? What does gmxcheck tell you about > each of them? It would seem that the simulation did not run long enough for > new .cpt files to be generated, or there was otherwise some problem with > writing the new file. You should not need a new .tpr file if you have not > yet completed the required 20 ns. See here: > > http://www.gromacs.org/Documentation/How-tos/Extending_Simulations > > -Justin > >> Please help. >> >> Thanks, >> >> Ram >> >> >> >> >> On Fri, Nov 6, 2009 at 10:15 PM, ram bio wrote: >>> >>> Dear Justin, >>> >>> Thanks for the information regarding the bug, will try the solutions >>> in the site. >>> >>> Ram >>> >>> On Fri, Nov 6, 2009 at 8:42 PM, Justin A. Lemkul wrote: ram bio wrote: > > Dear Gromacs users, > > I am running a protein-lipid bilayer simulation for 20ns. I am using > Gromacs version 4.0.5 and when i want to continue the mdrun using > -append command , I am getting an error as follows: > > Getting Loaded... > Reading file md20.tpr, VERSION 4.0.5 (single precision) > > Reading checkpoint file state.cpt generated: Fri Nov 6 15:22:25 2009 > > > --- > Program mdrun, VERSION 4.0.5 > Source code file: checkpoint.c, line: 1248 > > Fatal error: > Truncation of file traj.trr failed. > > Please suugest me how to overcome this error and continue the mdrun. > http://bugzilla.gromacs.org/show_bug.cgi?id=341 I believe this bug has been fixed in the development version (available through git). -Justin > Thanks, > > Ram > ___ > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scho
Re: [gmx-users] Truncation of file traj.trr failed
ram bio wrote: Dear Justin, As per the suggestions in the bug, i changed the line in src/gmxlib/checkpoint.c file on the cluster: from outputfiles[i].offset = ( ((off_t) offset_high) << 32 )| ( (off_t) offset_low ); to outputfiles[i].offset = ( ((off_t) offset_high) << 32 )| ( (off_t) offset_low & mask ); and was able to use the -append option, my command was mpiexec -np 4 /usr/local/gromacs/bin/mdrun -v -g $myjob.log -s md20.tpr -cpi state.cpt -append and this run generated another 3ns production data (from the step 2928600 - 590) and thus increasing the size of trr file to 4.8 GB from 2.1 GB, because my simulation is for 20ns, i submitted one more job with the same command after completing the 5.9 ns, So the job crashed again, then? mpiexec -np 4 /usr/local/gromacs/bin/mdrun -v -g $myjob.log -s md20.tpr -cpi state.cpt -append now again the job is starting from same step 2928600, i also tried using the command mpiexec -np 4 /usr/local/gromacs/bin/mdrun -v -g $myjob.log -s md20.tpr -cpi state_prev.cpt -append here also the output is same that is starting from 2928600 step, i want to continue the run from 590 step, please let me know how to proceed, do i have to generate a new .tpr file (my mdp file is defined for 20 ns and the output is md20.tpr) or can i use the same tpr file (md20.tpr) or i require to change the command to continue.. Were new .cpt files actually written? What does gmxcheck tell you about each of them? It would seem that the simulation did not run long enough for new .cpt files to be generated, or there was otherwise some problem with writing the new file. You should not need a new .tpr file if you have not yet completed the required 20 ns. See here: http://www.gromacs.org/Documentation/How-tos/Extending_Simulations -Justin Please help. Thanks, Ram On Fri, Nov 6, 2009 at 10:15 PM, ram bio wrote: Dear Justin, Thanks for the information regarding the bug, will try the solutions in the site. Ram On Fri, Nov 6, 2009 at 8:42 PM, Justin A. Lemkul wrote: ram bio wrote: Dear Gromacs users, I am running a protein-lipid bilayer simulation for 20ns. I am using Gromacs version 4.0.5 and when i want to continue the mdrun using -append command , I am getting an error as follows: Getting Loaded... Reading file md20.tpr, VERSION 4.0.5 (single precision) Reading checkpoint file state.cpt generated: Fri Nov 6 15:22:25 2009 --- Program mdrun, VERSION 4.0.5 Source code file: checkpoint.c, line: 1248 Fatal error: Truncation of file traj.trr failed. Please suugest me how to overcome this error and continue the mdrun. http://bugzilla.gromacs.org/show_bug.cgi?id=341 I believe this bug has been fixed in the development version (available through git). -Justin Thanks, Ram ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Truncation of file traj.trr failed
Dear Justin, As per the suggestions in the bug, i changed the line in src/gmxlib/checkpoint.c file on the cluster: from outputfiles[i].offset = ( ((off_t) offset_high) << 32 )| ( (off_t) offset_low ); to outputfiles[i].offset = ( ((off_t) offset_high) << 32 )| ( (off_t) offset_low & mask ); and was able to use the -append option, my command was mpiexec -np 4 /usr/local/gromacs/bin/mdrun -v -g $myjob.log -s md20.tpr -cpi state.cpt -append and this run generated another 3ns production data (from the step 2928600 - 590) and thus increasing the size of trr file to 4.8 GB from 2.1 GB, because my simulation is for 20ns, i submitted one more job with the same command after completing the 5.9 ns, mpiexec -np 4 /usr/local/gromacs/bin/mdrun -v -g $myjob.log -s md20.tpr -cpi state.cpt -append now again the job is starting from same step 2928600, i also tried using the command mpiexec -np 4 /usr/local/gromacs/bin/mdrun -v -g $myjob.log -s md20.tpr -cpi state_prev.cpt -append here also the output is same that is starting from 2928600 step, i want to continue the run from 590 step, please let me know how to proceed, do i have to generate a new .tpr file (my mdp file is defined for 20 ns and the output is md20.tpr) or can i use the same tpr file (md20.tpr) or i require to change the command to continue.. Please help. Thanks, Ram On Fri, Nov 6, 2009 at 10:15 PM, ram bio wrote: > Dear Justin, > > Thanks for the information regarding the bug, will try the solutions > in the site. > > Ram > > On Fri, Nov 6, 2009 at 8:42 PM, Justin A. Lemkul wrote: >> >> >> ram bio wrote: >>> >>> Dear Gromacs users, >>> >>> I am running a protein-lipid bilayer simulation for 20ns. I am using >>> Gromacs version 4.0.5 and when i want to continue the mdrun using >>> -append command , I am getting an error as follows: >>> >>> Getting Loaded... >>> Reading file md20.tpr, VERSION 4.0.5 (single precision) >>> >>> Reading checkpoint file state.cpt generated: Fri Nov 6 15:22:25 2009 >>> >>> >>> --- >>> Program mdrun, VERSION 4.0.5 >>> Source code file: checkpoint.c, line: 1248 >>> >>> Fatal error: >>> Truncation of file traj.trr failed. >>> >>> Please suugest me how to overcome this error and continue the mdrun. >>> >> >> http://bugzilla.gromacs.org/show_bug.cgi?id=341 >> >> I believe this bug has been fixed in the development version (available >> through git). >> >> -Justin >> >>> Thanks, >>> >>> Ram >>> ___ >>> gmx-users mailing listgmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/search before posting! >>> Please don't post (un)subscribe requests to the list. Use the www >>> interface or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> >> -- >> >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> 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/search before posting! >> Please don't post (un)subscribe requests to the list. Use the www interface >> or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] converting all-atom pdb to cg.pdb
I would appreciate very much that a stable version of the awk script is posted if my corrections were incorrect. Replacement in the martini web page would also be appreciated because one normally trusts in what is officially posted. Sure, but this isn't the forum best suited to communicating with the people who can make that fix. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] converting all-atom pdb to cg.pdb
Francesco Pietra wrote:
I corrected the awk script as indicated (attached here)
With input
ATOM 1 N LEU 1 153.242 64.673 95.851 0.00 0.00 N
ATOM 2 CA LEU 1 154.534 64.963 95.169 0.00 0.00 C
..
the output
ATOM 2 BN0 LEU 1 154.534 64.963 95.169 0.00 0.00
ATOM 4 SC1 LEU 1 156.589 66.550 95.065 0.00 0.00
is correct, the cgpdb file opens correctly in viewers, but there are
contacts, which gromacs was unable to relax at the relaxation stage
(nor it was at the all-atoms stage of the input file). Therefore I
relaxed the all-atoms input file with AMBER until no contacts at 0.8A
VDW, then repeated the awk script with the relaxed pdb file. Input
ATOM 1 N LEU A 1 153.242 64.673 95.851 0.00 0.00 N
ATOM 2 CA LEU A 1 154.534 64.963 95.169 0.00 0.00 C
.
the output
ATOM 2 BN0 LEU 0 1.000 154.534 64.963 95.17 0.00
ATOM 4 SC1 LEU 0 1.000 156.589 66.550 95.06 0.00
.
is grossly incorrect. Notice that both input files above give correct
psf and cg pdb files with VMD, just to say that the files are correct
pdb layout.
I was unable to understand why the awk script one time works, another
time not, just when I have a relxed file.
Because now you have a chain identifier, a case that I believe I mentioned last
time. If you look at the script, the pattern matching expects a numeric field
after the residue name; in the case of a chain identifier, this is not true and
the script returns a zero instead of the actual residue number. Note too that
in the output, every field is shifted exactly by one place as a result.
-Justin
I would appreciate very much that a stable version of the awk script
is posted if my corrections were incorrect. Replacement in the martini
web page would also be appreciated because one normally trusts in what
is officially posted.
thanks
francesco pietra
On Mon, Nov 9, 2009 at 12:58 PM, Justin A. Lemkul wrote:
Francesco Pietra wrote:
Does the atom2cg_v2.1.awk require the indication of the subunit (A, B,
C, etc) in the pdb file of a multimeric protein?
From
ATOM 1 N LEU 1 153.242 64.673 95.851 0.00 0.00
N
ATOM 2 CA LEU 1 154.534 64.963 95.169 0.00 0.00
C
ATOM 3 CB LEU 1 155.257 66.191 95.767 0.00 0.00
C
ATOM 4 CG LEU 1 156.589 66.550 95.065 0.00 0.00
C
ATOM 5 CD1 LEU 1 156.406 66.834 93.574 0.00 0.00
C
ATOM 6 CD2 LEU 1 157.222 67.770 95.727 0.00 0.00
C
ATOM 7 C LEU 1 155.425 63.717 95.081 0.00 0.00
C
ATOM 8 O LEU 1 155.371 63.026 94.063 0.00 0.00
O
ATOM 9 N SER 2 156.233 63.409 96.105 0.00 0.00
N
I get
ATOM 2 BN0 LEU 154.534 64.963 95.169 0.000 0.00 0.00
ATOM 4 SC1 LEU 156.589 66.550 95.065 0.000 0.00 0.00
ATOM 10 BN0 SER 157.124 62.235 96.094 0.000 0.00 0.00
i.e., weird residue numbers.
The awk script simply copies the information from one line to the new file,
using the old atom numbers. You can use genconf -renumber to fix this. The
reason why the residue number isn't being written is because there is a
problem with the atom2cg script that I have posted here a number of times.
For example, you need to fix each line of the script:
OLD LINE
if($1=="ATOM" && $4=="ARG" && $3=="CA")
printf("%4s %5i %4s %3s %4s%8.3f%8.3f%8.3f%6.2f%6.2f\n",$1, $2,
"BN0", $4, $6, $7, $8, $9,$10,$11);
FIXED LINE
if($1=="ATOM" && $4=="ARG" && $3=="CA")
printf("%4s %5i %4s %3s %4i%8.3f%8.3f%8.3f%6.2f%6.2f\n",$1, $2,
"BN0", $4, $5, $6, $7, $8, $9,$10,$11);
In another case (coming from AMBER, where the subunit indication is
omitted) with the subunit indicated, the residue numbers in the cg
file are correct. I don't see any other difference between the two
starting files. Or should I look for a different cause.
Then that's simply a matter of luck :) The print statements in the original
awk script do not expect chain identifiers, so the printing worked due to
the extra field.
-Justin
thanks
francesco pietra
...
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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/search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface
or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
=
Re: [gmx-users] converting all-atom pdb to cg.pdb
I corrected the awk script as indicated (attached here)
With input
ATOM 1 N LEU 1 153.242 64.673 95.851 0.00 0.00 N
ATOM 2 CA LEU 1 154.534 64.963 95.169 0.00 0.00 C
..
the output
ATOM 2 BN0 LEU 1 154.534 64.963 95.169 0.00 0.00
ATOM 4 SC1 LEU 1 156.589 66.550 95.065 0.00 0.00
is correct, the cgpdb file opens correctly in viewers, but there are
contacts, which gromacs was unable to relax at the relaxation stage
(nor it was at the all-atoms stage of the input file). Therefore I
relaxed the all-atoms input file with AMBER until no contacts at 0.8A
VDW, then repeated the awk script with the relaxed pdb file. Input
ATOM 1 N LEU A 1 153.242 64.673 95.851 0.00 0.00 N
ATOM 2 CA LEU A 1 154.534 64.963 95.169 0.00 0.00 C
.
the output
ATOM 2 BN0 LEU 0 1.000 154.534 64.963 95.17 0.00
ATOM 4 SC1 LEU 0 1.000 156.589 66.550 95.06 0.00
.
is grossly incorrect. Notice that both input files above give correct
psf and cg pdb files with VMD, just to say that the files are correct
pdb layout.
I was unable to understand why the awk script one time works, another
time not, just when I have a relxed file.
I would appreciate very much that a stable version of the awk script
is posted if my corrections were incorrect. Replacement in the martini
web page would also be appreciated because one normally trusts in what
is officially posted.
thanks
francesco pietra
On Mon, Nov 9, 2009 at 12:58 PM, Justin A. Lemkul wrote:
>
>
> Francesco Pietra wrote:
>>
>> Does the atom2cg_v2.1.awk require the indication of the subunit (A, B,
>> C, etc) in the pdb file of a multimeric protein?
>>
>> From
>>
>> ATOM 1 N LEU 1 153.242 64.673 95.851 0.00 0.00
>> N
>> ATOM 2 CA LEU 1 154.534 64.963 95.169 0.00 0.00
>> C
>> ATOM 3 CB LEU 1 155.257 66.191 95.767 0.00 0.00
>> C
>> ATOM 4 CG LEU 1 156.589 66.550 95.065 0.00 0.00
>> C
>> ATOM 5 CD1 LEU 1 156.406 66.834 93.574 0.00 0.00
>> C
>> ATOM 6 CD2 LEU 1 157.222 67.770 95.727 0.00 0.00
>> C
>> ATOM 7 C LEU 1 155.425 63.717 95.081 0.00 0.00
>> C
>> ATOM 8 O LEU 1 155.371 63.026 94.063 0.00 0.00
>> O
>> ATOM 9 N SER 2 156.233 63.409 96.105 0.00 0.00
>> N
>>
>> I get
>>
>> ATOM 2 BN0 LEU 154.534 64.963 95.169 0.000 0.00 0.00
>> ATOM 4 SC1 LEU 156.589 66.550 95.065 0.000 0.00 0.00
>> ATOM 10 BN0 SER 157.124 62.235 96.094 0.000 0.00 0.00
>>
>> i.e., weird residue numbers.
>>
>
> The awk script simply copies the information from one line to the new file,
> using the old atom numbers. You can use genconf -renumber to fix this. The
> reason why the residue number isn't being written is because there is a
> problem with the atom2cg script that I have posted here a number of times.
> For example, you need to fix each line of the script:
>
> OLD LINE
> if($1=="ATOM" && $4=="ARG" && $3=="CA")
> printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
> "BN0", $4, $6, $7, $8, $9,$10,$11);
>
> FIXED LINE
> if($1=="ATOM" && $4=="ARG" && $3=="CA")
> printf("%4s %5i %4s %3s %4i %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
> "BN0", $4, $5, $6, $7, $8, $9,$10,$11);
>
>
>> In another case (coming from AMBER, where the subunit indication is
>> omitted) with the subunit indicated, the residue numbers in the cg
>> file are correct. I don't see any other difference between the two
>> starting files. Or should I look for a different cause.
>>
>
> Then that's simply a matter of luck :) The print statements in the original
> awk script do not expect chain identifiers, so the printing worked due to
> the extra field.
>
> -Justin
>
>> thanks
>>
>> francesco pietra
>> ...
>
> --
>
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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 list gmx-us...@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
atom2cg_v2.1.awk
Description: application/awk
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Please don't post (un)subscribe requests to the l
Re: [gmx-users] LJ scaling and EnerPress correction
Antonia V. wrote: Dear all, I am trying to simulate a two component system, and I would like to ask you the two following questions: 1) Is it possible to use a different scaling factor (for the LJ and the electrostatics) for each component? Not natively. How would you like to treat non-bonded interactions between atoms belonging to different components? 2) Is it possible to use energy and pressure correction only for the one of the two components and not for the other? No. Why would you want to do this? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: gmx-users Digest, Vol 67, Issue 60
pawan raghav wrote: Dear, Your tutorial for windows are lacking of proper guidence. You should post the steps to use it to make it more user friendly. As I have tried from last two months but after installing it I really don't know to execute commands on windows. If you can guide me then why don't you not tell me the steps for using it on windows. I endorse Tsjerk's comments wholeheartedly. I don't know why you didn't search the GROMACS website for steps for using it on Windows, as I've had a Cygwin-installation HOWTO there for several years. :-) Every one of the "how to get help for GROMACS" pages suggests searching web pages and Google before posting on these lists, but many people overlook those... That usually costs them time and effort. If you really think the available installation documents lack proper guidance, then please feel free to suggest improvements. We're all volunteers, but people might be motivated to fix things if the target audience can convince them that things aren't documented well enough. That process takes more effort than making general negative comments, however :-) Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] LJ scaling and EnerPress correction
Dear all, I am trying to simulate a two component system, and I would like to ask you the two following questions: 1) Is it possible to use a different scaling factor (for the LJ and the electrostatics) for each component? 2) Is it possible to use energy and pressure correction only for the one of the two components and not for the other? Thank you for your help, Antonia Keep your friends updated— even when you’re not signed in. _ Windows Live: Make it easier for your friends to see what you’re up to on Facebook. http://www.microsoft.com/middleeast/windows/windowslive/see-it-in-action/social-network-basics.aspx?ocid=PID23461::T:WLMTAGL:ON:WL:en-xm:SI_SB_2:092009-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Installation on Windows
Hi Pawan, It may be unintentional, but your post is rather impolite. Do mind that the people that answer questions here have no obligation to help you. Nobody should put any effort in making something more user friendly, unless it is part of their job, e.g. for classes. You can ask if somebody would have the kindness to put such effort in. Installing under windows is usually considered awkward. The best way, as is indicated in the pages that Mark referred to - not his tutorial by any means -, is to install it under a *nix emulator like Cygwin. That brings in the need to know a bit about a *nix environment. Plenty of tutorial material for that out there, but that has nothing to do with Gromacs per se. That should be your effort. I can understand that it raises frustration that you can't get it to work, but at this point, that stands apart from Gromacs. There are other fora for help on getting started with *nix, cygwin, etc. Cheers, Tsjerk On Tue, Nov 10, 2009 at 9:03 AM, pawan raghav wrote: > Dear, > > Your tutorial for windows are lacking of proper guidence. You should post > the steps to use it to make it more user friendly. > > As I have tried from last two months but after installing it I really don't > know to execute commands on windows. If you can guide me then why don't you > not tell me the steps for using it on windows. -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: gmx-users Digest, Vol 67, Issue 60
rface > >> or send it to gmx-users-requ...@gromacs.org. > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >> > > > > > > > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > > -- > > Message: 3 > Date: Mon, 9 Nov 2009 22:10:22 -0500 > From: Jack Shultz > Subject: Re: [gmx-users] Missing H from residue > To: jalem...@vt.edu, Discussion list for GROMACS users > > Message-ID: ><6c65435e0911091910r7c932c23l2a2814b72d8be...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Thanks Justin! Got it now. > > On Mon, Nov 9, 2009 at 10:00 PM, Justin A. Lemkul wrote: > > > > > > Jack Shultz wrote: > >> > >> On Mon, Nov 9, 2009 at 8:35 PM, Justin A. Lemkul > wrote: > >>> > >>> Jack Shultz wrote: > >>> > >>> > >>> > >>>> --- > >>>> Program pdb2gmx, VERSION 4.0.5 > >>>> Source code file: pdb2gmx.c, line: 429 > >>>> > >>>> Fatal error: > >>>> Atom O in residue CARG 244 not found in rtp entry with 25 atoms > >>>>while sorting atoms > >>>> --- > >>>> > >>>> But we got an O here > >>>> ATOM 3822 O CARG 153 -4.455 -21.080 2.791 1.00 0.00 > >>>> O > >>>> > >>> The error is not telling you that the O atom is missing from the .pdb > >>> file; > >>> it is telling you that it is present in the .pdb, but not in the .rtp > >>> entry. > >>> Look at the .rtp entry for CARG > >> > >> [ CARG ] > >> [ atoms ] > >> Namber99_34 -0.34810 1 > >> Hamber99_17 0.27640 2 > >>CAamber99_11 -0.30680 3 > >>HAamber99_19 0.14470 4 > >>CBamber99_11 -0.03740 5 > >> HB1amber99_18 0.03710 6 > >> HB2amber99_18 0.03710 7 > >>CGamber99_11 0.07440 8 > >> HG1amber99_18 0.01850 9 > >> HG2amber99_18 0.0185010 > >>CDamber99_11 0.1114011 > >> HD1amber99_19 0.0468012 > >> HD2amber99_19 0.0468013 > >>NEamber99_38 -0.5564014 > >>HEamber99_17 0.3479015 > >>CZamber99_30.8368016 > >> NH1amber99_38 -0.8737017 > >> HH11amber99_17 0.4493018 > >> HH12amber99_17 0.4493019 > >> NH2amber99_38 -0.8737020 > >> HH21amber99_17 0.4493021 > >> HH22amber99_17 0.4493022 > >> Camber99_20.8557023 > >> OC1amber99_45 -0.8266024 > >> OC2amber99_45 -0.8266025 > >> > >> - you should have an O1 and O2 atom for the > >> > >> I made the following modification > >> ATOM 1900 O1 CARG 153 -17.391 -20.267 11.508 1.00 0.00 > >> O > >> ATOM 1909 O2 CARG 153 -18.666 -19.390 13.107 1.00 0.00 > >> O > >> > > > > Forgive my typo, what I meant was OC1 and OC2. You must always make sure > > the atoms in the structure file match those expected by the .rtp > file. You > > need OC1 and OC2. > > > > -Justin > > > >> > >> --- > >> Program pdb2gmx, VERSION 4.0.5 > >> Source code file: pdb2gmx.c, line: 429 > >> > >> Fatal error: > >> Atom O in residue CARG 122 not found in rtp entry with 25 atoms > >> while sorting atoms > >> --- > >> > >> > >>> C-terminal carboxylate. > >>> > >>> -Justin > >>> > >>> -- > >>> > >>> > >>> Justin A. Lemkul > >>> Ph.D. Candidate > >>> ICTAS Doctoral Scholar > >>> Department of Biochemistry > >>> Virginia Tech &g
