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

Vitaly Chaban vvchaban at gmail.com
Fri Jun 27 13:41:46 CEST 2008

I think Bhanu was embarrassed that one part of his protein was from one side and the
remainder was from another. Of course, there cannot be a state
'outside' in reality.

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

TW> 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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