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 <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users <gmx-users@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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> wrote:
On Tue, 22 Apr 2008 14:14:19 -0700
"Ilya Chorny" <[EMAIL PROTECTED]> 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.
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