[gmx-users] How to recenter solvent around solute

[Justin A. Lemkul]

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.

-Justin

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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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