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

Vitaly Chaban vvchaban at gmail.com
Fri Jun 27 12:58:46 CEST 2008

> 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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