[gmx-users] optimum acceptance ratio for REMD
ben at reynwar.net
Thu Jan 12 19:42:03 CET 2012
I am currently puzzled by the emphasis on using an acceptance ratio of
around 0.2 for replica exchange simulations in the literature.
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
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?
More information about the gromacs.org_gmx-users