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 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 -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
