[gmx-users] Ligand moves out of box during EM steps

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Mar 22 07:54:05 CET 2006

Hi Raja,

Probably PBC. Nothing wrong, just visual. You can try to center your system
on the ligand before starting the simulation, which should keep it "in


On 3/22/06, raja <raja_28 at fastmail.us> wrote:
> I reposting the same query since not getting response for my previous
> posting. In short
> I am unable to restraint the ligand at its active site during
> minimization, though I used position restrints
> for all of the atom types of my ligand. At the end of simulation, it is
> jumping out of active site and located
> itself at the corner of the water box.
> Kindly provide me the solution to retain the ligand at its original
> position during minimization step!
> With thanks !
> B.Nataraj
> --
>   raja
>   raja_28 at fastmail.us
> --
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Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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