rabab,
justin mentioned the *gro file saved at the end of the simulation - the last
line contains the box dimensions.
you can extract them with g_energy:
g_energy -f your_edr_file -o your_output_file
and then selecting:
Box-X
Box-Y
Box-Z
good luck,
igor
Igor Marques
On Mon, Jul 25, 2011 at 5:07 PM, Rabab Toubar <rtou...@yahoo.com> wrote:
> Thanks Justin for your reply. But what is the extension of the output
> coordinate file. And for the .edr file it failed to open in windows; how can
> I possibly view it
>
> Thanks
> Rabab Toubar
>
>
>
> --- On Mon, 7/25/11, Justin A. Lemkul <jalem...@vt.edu> wrote:
>
> > From: Justin A. Lemkul <jalem...@vt.edu>
> > Subject: Re: [gmx-users] water box size from output files
> > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
> > Date: Monday, July 25, 2011, 11:15 AM
> >
> >
> > Rabab Toubar wrote:
> > > Hi
> > >
> > > I was wondering if there is a way to determine the
> > water box size from the output files after the simulation
> > run is over
> > >
> >
> > Box vectors are printed to the output coordinate file
> > (final snapshot) and can be extracted from along the
> > trajectory from the .edr file.
> >
> > -Justin
> >
> > -- ========================================
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
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