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] 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
