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

Xavier Periole X.Periole at rug.nl
Tue Apr 22 23:59:13 CEST 2008

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

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