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 >
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