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

[Ilya Chorny]

So I got it to work for my trimer by doing the following.
1.) trjconv -f *.xtc -s *.tpr -pbc nojump -o out.xtc
2.) trjconv -f out.xtc -s *.tpr -pbc mol -center -boxcenter rect

The first step unwraps the whole trajectory and the second step wraps it
back up.

Cheers,

Ilya


-- 
Ilya Chorny Ph.D.

On Tue, Apr 22, 2008 at 4:30 PM, Alan Dodd <anoddlad at yahoo.com> wrote:

> I've often found it necessary to do multiple trjconv steps to get the
> result I want.  So in this case, I'd probably make sure my protein is
> genuinely centered in the box, then take that output .xtc and then make sure
> everything is whole and approximately in the box (-pbc whole).
>
>
>  ----- Original Message ----
> From: Ilya Chorny <ichorny at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Tuesday, April 22, 2008 11:52:23 PM
> Subject: Re: [gmx-users] How to center my trimer in my simulation box.
>
> 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
> > > -----------------------------------------------------
> > > _______________________________________________
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> >
> >
> >
> > --
> > Ilya Chorny Ph.D.
> >
>
>
>
> --
> Ilya Chorny Ph.D.
>
>
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-- 
Ilya Chorny Ph.D.
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