[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:
> 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
The documentation must remain somewhat generic, as there are a number of
specialty systems that can be considered.
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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