[gmx-users] Imaging in PBC simulations

Jochen Hub jhub at gwdg.de
Mon Apr 24 16:48:00 CEST 2006

Martin LEPSIK wrote:

> Dear GROMACS users,
> I would like to ask you maybe a trivial question: What is the best way 
> to image a protein with a ligand inside
> a triclinic water box?
> I run an MD in GMX-3.3 with nstcomm=1, "comm_grps" and "comm_mode" not 
> set. I watch the movie in VMD,
> loading first a starting gro and than the trr. The problem is that the 
> protein creeps out of the box (the same happens
> when using ngmx).
> I have tried various variants of post-processing using trjconv -fit 
> (translation) -pbc (inbox, whole) -center (tric),
> groups for fitting: protein or system. But in any case, the result is 
> the same.
> Could you please advice me how to solve this? Whether it is better to 
> include some parameter for
> mdrun or to post-process in a different way?
> Looking forward to hearing from you.
> Yours sincerely,
> Martin Lepsik
You can either
 use comm_grps = Protein and comm_mode = Linear
use trjconv with the -fit option and fit your protein on the starting 
position after finishing the simulation.

Cheers, Jochen

Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de

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