[gmx-users] How to generate xvg files

[Amit Choubey]

On Tue, Nov 10, 2009 at 7:02 PM, Jack Shultz <js at 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.amit at gmail.com> wrote:
> >
> >
> > On Tue, Nov 10, 2009 at 6:31 PM, Jack Shultz <js at 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.amit at gmail.com>
> wrote:
> >> >
> >> >
> >> > On Tue, Nov 10, 2009 at 6:11 PM, Jack Shultz
> >> > <js at 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
> >> >> --
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> >> >
> >> >
> >> > --
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> >>
> >>
> >>
> >> --
> >> Jack
> >>
> >> http://drugdiscoveryathome.com
> >> http://hydrogenathome.org
> >> --
> >> gmx-users mailing list    gmx-users at gromacs.org
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> >
> >
> > --
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>
>
>
> --
> Jack
>
> http://drugdiscoveryathome.com
> http://hydrogenathome.org
> --
> gmx-users mailing list    gmx-users at gromacs.org
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> Please search the archive at http://www.gromacs.org/search before posting!
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