[gmx-users] trjconv, -pbc whole, and Max OS X?

[Tsjerk Wassenaar]

Hi Emma,

When using -pbc whole you should provide a run input (.tpr) file. But under
normal circumstances your molecules wouldn't be broken in an original .trr
file. You could try to run trjconv without any particular option: trjconv -f
input.trr -o output.gro -s reference.tpr

Cheers,

Tsjerk

On 11/17/05, Viswanadham Sridhara <muta.mestri at gmail.com> wrote:
>
> What about the initial structure of the run?
>
> On 11/17/05, Emma Falck <efalck at cc.hut.fi> wrote:
> >
> > Hi,
> >
> > My problem is with the trjconv command. I am trying to convert a
> > trajectory
> > in the .trr format to a trajectory in the .gro format, such that the
> > molecules are whole in the resulting trajectory. To do so, I use trjconv
> >
> > with the option '-pbc whole'. Even so, my molecules -- both lipids and
> > water molecules -- are broken in the resulting .gro file.
> >
> > I recently installed Gromacs 3.3 to my PowerBook, that runs OS X 10.4.
> > I did not compile Gromacs from the source, but used the OS X package
> > provided
> > on the gromacs pages.
> >
> > Has anyone else had related/similar problems with trjconv, in particular
> > with
> > OS X?
> >
> > Best regards,
> >
> > Emma
> >
> > --
> > Dr. Emma Falck
> > Beckman Institute, UIUC
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>
>
> --
> Viswanadham Sridhara,
> Graduate Research Assistant,
> Old Dominion University, "VIRGINIA".
>
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>


--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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