[gmx-users] How to recenter solvent around solute

Justin A. Lemkul jalemkul at vt.edu
Sat May 7 17:02:15 CEST 2011

Dimitar Pachov wrote:
> Hello,
> I have performed simulations of protein+ligands (solute) in truncated 
> octahedral unit cell of waters (solvent). I would like to retain the 
> shape of unit cell and have the solute centered in such a way as to be 
> completely surrounded by solvent.  At this point, I cannot achieve this 
> although I have exhausted my knowledge about using the trjconv options. 
> My question is:
> 1. How can one recenter solvent around solute and at the same time keep 
> the original unit shape?
> I used the following command to get this picture:
> trjconv -f run.xtc -s run.tpr -n index-all.ndx -o traj/run-test.xtc -pbc 
> mol -center -ur compact

Use -ur tric instead of -ur compact.


> where for centering the solute was used and the whole system was saved 
> to the output trajectory. 
> Thanks,
> Dimitar


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


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