[gmx-users] protein domain separate
Mark.Abraham at anu.edu.au
Tue Oct 13 15:58:52 CEST 2009
> I want to do MD on a two-domain protein (Protein A, Protein B). After doning
> position restranit for 20 ps, the final structure separated. How could I
> keep these 2 domain close to each other during whole MD run.
Check that they're not separated because of a PBC artefact (try trjconv
-compact or something). If the positions were really restrained, they
can't actually have separated.
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