[gmx-users] Getting out of the box!!!

Tsjerk Wassenaar tsjerkw at gmail.com
Wed May 10 10:43:56 CEST 2006


Have you considered reading the FAQ, searching the mailing list, reading the
manual or just paying attention? Just yesterday there was mention of a
ligand jumping out of the box, to which several replies were given and your
exact question is asked on this list at least every month!

I'll keep my temper. It's just due to the periodic boundary conditions,
nothing wrong, you can use trjconv with option -pbc nojump afterwards or you
can set comm_mode to linear with the protein as comm_group. Now please read
the manual on periodic boundary conditions and for further reference search
the mail list (e.g. "periodic boundary conditions", "PBC", "jumping",


On 5/10/06, Marcelo Fabricio Masman <mmasman at gmail.com> wrote:
> Hello gmx users:
> I am running a very common MD simulation and the protein system is getting
> OUT of the box after approximately 200 ps. I have tried several things.
> Does it happen very frequently? (common mistake)
> Is there any way to keep, during the whole calculation, the protein system
> into the center of the box?
> What could I do for avoiding this phenomenon?
> Thanks in advance.
> Marcelo
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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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