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 <[email protected]> wrote: > > > On Tue, Nov 10, 2009 at 6:31 PM, Jack Shultz <[email protected]> > 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 <[email protected]> wrote: >> > >> > >> > On Tue, Nov 10, 2009 at 6:11 PM, Jack Shultz >> > <[email protected]> >> > 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 [email protected] >> >> 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 [email protected]. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > >> > >> > -- >> > gmx-users mailing list [email protected] >> > 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 [email protected]. >> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > >> >> >> >> -- >> Jack >> >> http://drugdiscoveryathome.com >> http://hydrogenathome.org >> -- >> gmx-users mailing list [email protected] >> 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 [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
