[gmx-users] Imaging in PBC simulations
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
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.
Martin Lepsik, Ph.D.
Laboratoire de Dynamique Moléculaire (LDM)
Institut de Biologie Structurale
41, rue Jules Horowitz
38027 Grenoble Cedex 1, France
e-mail: martin.lepsik at ibs.fr
More information about the gromacs.org_gmx-users