Dear Jochen and Tamas,
thanks for your replies. I tried both, the "trjconv -fit" postprocessing
and setting "comm_mode" for mdrun and actually only the latter worked
fine. In the former, protein drifts toward the box side and jumps out
for some frames, leaving its bound ions inside the box. Better to remove
translation during the run.
All the best,
Martin
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 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
or
use trjconv with the -fit option and fit your protein on the starting
position after finishing the simulation.
Cheers, Jochen
--
--------------------------
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: [EMAIL PROTECTED]
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