[gmx-users] Replica exchange and freeze groups?
David van der Spoel
spoel at xray.bmc.uu.se
Sun Nov 12 21:07:18 CET 2006
Marc Baaden wrote:
> I do wonder whether replica exchange as implemented in Gromacs is
> compatible with freezing part of a system. What I want to do is to
> equilibrate a sub-part (18k atoms) of a large system (340k atoms)
> by freezing the 322k surrounding atoms and doing replica exchange
> on the "small" 18k atom system.
> Is there any trouble to be expected for combining these two options?
> Does anybody have experience with such an approach?
> Thanks in advance,
> Marc Baaden
I don't see why it shouldn't work, but be careful when combining too
many things like pressure coupling and constraints and freezing.
Test it on a smaller system first.
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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