[gmx-users] RE: Protein is moving out of box.

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Jun 27 13:28:18 CEST 2008


That doesn't necessarily "fix" the "problem". Which position of the
protein is taken as a reference depends on the position of the first
atom. Gromacs wants to have the first atom of a molecule in the
rectangular unit cell at the origin. Even if you set comm removal for
the group, the initial orientation and/or conformational changes may
cause the first atom to jump over the boundaries.

Whatever the case, everyone doing MD simulations should be aware of
periodic boundary conditions. There is no "outside of the box".


On Fri, Jun 27, 2008 at 12:58 PM, Vitaly Chaban <vvchaban at gmail.com> wrote:
>> am new to Gromacs. I tried a 10 ps simulation with a protein and after the
>> run, the protein came out of the box.. is it good or bad?
> Its terrible. If it runs away you'll never have a new such frolicsome protein... ;)
>>  How can I keep the protein in the box?
> Just fix it. In .mdp file write comm-grps = _YOUR_PROTEIN_GROUP_
> --
> Vitaly V. Chaban
> School of Chemistry
> National University of Kharkiv
> Svobody sq.,4, Kharkiv 61077, Ukraine
> email: chaban at univer.kharkov.ua
> skype: vvchaban
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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