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

Justin A. Lemkul jalemkul at vt.edu
Fri Jun 15 18:43:56 CEST 2012

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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