[gmx-users] protein near the edges of simulation box

Shima Arasteh shima_arasteh2001 at yahoo.com
Fri Jun 15 18:52:51 CEST 2012

Oh, Thanks a lot. That is really  kind of you.


 From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Friday, June 15, 2012 9:13 PM
Subject: Re: [gmx-users] protein near the edges of simulation box

On 6/15/12 12:41 PM, Shima Arasteh wrote:
> Thanks.
> Sorry, what do you mean by trajectory A and B?

It's just a generic example.  To be absolutely clear, let's say you have a trajectory named "md.xtc" that mdrun produces.  That trajectory will have molecules that diffuse all over the place.  You load it into VMD, and it's probably not convenient to look at.  If you then run trjconv:

trjconv -s md.tpr -f md.xtc -center -o centered.xtc
(choose an appropriate group, like Protein, to center)

Then you have to close VMD and load it completely over again, supplying "centered.xtc" as the data for your initial configuration.


-- ========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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