On Tue, Nov 10, 2009 at 7:02 PM, Jack Shultz <j...@drugdiscoveryathome.com>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 <kgp.a...@gmail.com> wrote: > > > > > > On Tue, Nov 10, 2009 at 6:31 PM, Jack Shultz <j...@drugdiscoveryathome.com > > > > 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 <kgp.a...@gmail.com> > wrote: > >> > > >> > > >> > On Tue, Nov 10, 2009 at 6:11 PM, Jack Shultz > >> > <j...@drugdiscoveryathome.com> > >> > 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-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 list gmx-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 list gmx-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 list gmx-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 list gmx-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 list gmx-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