[gmx-users] How to recenter solvent around solute

Dimitar Pachov dpachov at brandeis.edu
Sat May 7 14:49:12 CEST 2011


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

where for centering the solute was used and the whole system was saved to
the output trajectory.

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