[gmx-users] Imaging in PBC simulations

Martin LEPSIK martin.lepsik at ibs.fr
Mon Apr 24 15:41:56 CEST 2006

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

Martin Lepsik, Ph.D. 
Laboratoire de Dynamique Moléculaire (LDM)
Institut de Biologie Structurale
41, rue Jules Horowitz
38027 Grenoble Cedex 1, France
tel: +33-4-3878-4780
e-mail: martin.lepsik at ibs.fr

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