[gmx-users] How to recenter solvent around solute

Justin A. Lemkul jalemkul at vt.edu
Sun May 8 03:45:58 CEST 2011

Dimitar Pachov wrote:
> On Sat, May 7, 2011 at 11:02 AM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
>     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.
> This does not work. Neither is the solute always surrounded by solvent 
> for every frame (it goes out of the box) nor is the original unit cell 
> (truncated octahedron) preserved. 

Please clarify - do you wish to maintain the original triclinic representation 
(as -ur tric does) or do you wish to see the octahedral representation (as -pbc 
mol -ur compact gives)?  My answer was based on your request to "keep the 
original unit shape."

> I don't understand how one can achieve this, and if there is a way to do 
> it, why it has not been clearly explained elsewhere.

For complicated systems (or sometimes even for simple ones), it is quite common 
that multiple iterations of trjconv are necessary.  A suggested workflow is 
indeed documented:


The documentation must remain somewhat generic, as there are a number of 
specialty systems that can be considered.



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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