You can use belly (bellymask, etc.), which keeps a subset (whatever you did
NOT specify) frozen while allowing everything else to move. However, I
don't think that method is very strongly endorsed by a lot of the
developers. It may not play nicely with other parts of the simulation, such
as pressure scaling and wrapping.
Good luck!
Jason
On Thu, Sep 23, 2010 at 11:46 AM, Laura Perissinotti <perissinotti.gmail.com
> wrote:
> Hi, I'm doing molecular dynamics (pmemd) for a dimer protein, each monomer
> has about 400 residues. I would like to know if it is possible to do the MD
> only for one monomer and keep the other frozen during MD (like a rigid
> body)
> in order to save computing time. If I apply restraints to the other
> monomer,
> I won' t save any time, Is that right?
> Thanks
> Laura.
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Sep 23 2010 - 09:30:16 PDT
