[gmx-users] How to center my trimer in my simulation box.

[Ilya Chorny]

So I got it to center my protein (using -pbc nojump)  and keep the trimer
and the membrane in tact but it completely destroyed my water. I was hoping
I could get the whole simulation box back with the protein in the center.
Is that possible?

Thanks,

Ilya


On Tue, Apr 22, 2008 at 3:25 PM, Ilya Chorny <ichorny at gmail.com> wrote:

> Just to clarify.
> I would run
>
> trjconv -f *.gro -s *.tpr -pbc nojump -o out.gro?
>
> What would I run next?
>
> Thanks,
>
> Ilya
>
>
> On Tue, Apr 22, 2008 at 2:59 PM, Xavier Periole <X.Periole at rug.nl> wrote:
>
> > On Tue, 22 Apr 2008 14:14:19 -0700
> >  "Ilya Chorny" <ichorny at gmail.com> wrote:
> >
> > > Hello,
> > >
> > > I am simulating a trimer in a membrane. In one of my simulation  two
> > > of the
> > > monomers are on one side of the box and the other monomer is on the
> > > other
> > > side of the box. I tried using trjconv to center the whole thing in
> > > the
> > > center of my simulation cell but have failed miserably. I also
> > > searched
> > > around for about an hour and could not find anything.
> > >
> > > I use trjconv -f *.gro -s *.tpr -center rect -pbc whole -o *.gro.
> > >
> > first run
> > trjconv -pbc nojump
> >
> > > Any advice?
> > >
> > > Thanks,
> > >
> > > Ilya
> > >
> > > --
> > > Ilya Chorny Ph.D.
> > >
> >
> > -----------------------------------------------------
> > XAvier Periole - PhD
> >
> > NMR & Molecular Dynamics Group
> > University of Groningen
> > The Netherlands
> > http://md.chem.rug.nl/~periole <http://md.chem.rug.nl/%7Eperiole>
> > -----------------------------------------------------
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>
>
>
> --
> Ilya Chorny Ph.D.
>



-- 
Ilya Chorny Ph.D.
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