Simulating Replica Exchange: Markov State Models, Proposal Schemes, and the Infinite Swapping Limit.

ABSTRACT: Replica exchange molecular dynamics is a multicanonical simulation technique commonly used to enhance the sampling of solvated biomolecules on rugged free energy landscapes. While replica exchange is relatively easy to implement, there are many unanswered questions about how to use this technique most efficiently, especially because it is frequently the case in practice that replica exchange simulations are not fully converged. A replica exchange cycle consists of a series of molecular dynamics steps of a set of replicas moving under different Hamiltonians or at different thermodynamic states followed by one or more replica exchange attempts to swap replicas among the different states. How the replica exchange cycle is constructed affects how rapidly the system equilibrates. We have constr

SUBMITTER: Zhang BW 

PROVIDER: S-EPMC5001888 | biostudies-literature | 2016 Aug

REPOSITORIES: biostudies-literature