[gmx-users] protein domain separate

[Mark Abraham]

hazizian wrote:
> Hi 
> 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.

Mark