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

Alan Dodd anoddlad at yahoo.com
Wed Apr 23 01:30:41 CEST 2008

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?



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?



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:


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?



Ilya Chorny Ph.D.

XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
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