On 2012-01-12 19:42, Ben Reynwar wrote:
Hi all,
I am currently puzzled by the emphasis on using an acceptance ratio of
around 0.2 for replica exchange simulations in the literature.
This is bogus indeed.
You are correct. Many people prefer not to think.
What matters is that the time between exchanges is larger than the
relaxation, which hence is system dependent, and that you have
sufficient number of exchanges to equilibrate the T-dependent properties
(which can be challenging).
Our old paper is one of the few where this succeeded for a peptide
because it is so small :).
Marvin Seibert, Alexandra Patriksson, Berk Hess and David van der Spoel:
Reproducible polypeptide folding and structure prediction using
molecular dynamics simulations J. Mol. Biol. 354 pp. 173-183 (2005)
David van der Spoel and M. Marvin Seibert: Protein Folding Kinetics and
Thermodynamics from Atomistic Simulations Phys. Rev. Lett. 96 pp. 238102
(2006)
This optimum ratio is, as far as I understand, derived assuming that
the exchange attempt frequency is constant and that the protein
dynamics are not limiting the diffusion of a replica up and down
the temperature ladder.
In a real system there will be some time-scale associated with the
relaxation of the protein as it moves from one temperature to another.
The rate of diffusion of the replica on the temperature ladder could
potentially be limited by these protein dynamics or by the exchange
frequency.
If we are limited by the exchange frequency, then it would make sense
to decrease the interval between exchange attempts to the same
time-scale as the potential energy correlation time, and to choose the
number of replicas such that the acceptance ratio was around 0.2.
If we are limited by the protein dynamics then the exchange frequency
doesn't matter, so the acceptance ratio should have no effect (as
long, of course, as it isn't so low that the exchange frequency
becomes limiting). This would mean for simulations of large proteins where
the protein dynamics are limiting, we can slash the number of replicas
required for an efficient REMD simulation.
However, I haven't seen any simulations in the literature using very small
acceptance ratios, which makes me suspicious of my logic. Does anyone have
any thoughts on this?
Cheers,
Ben
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
[email protected] http://folding.bmc.uu.se
--
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