title: Serial replica exchange.
abstract: Parallel tempering (or the replica exchange method (REM)) is a powerful method for speeding up the sampling of conformational states of systems with rough energy landscapes, like proteins, where stable conformational states can be separated by large energy barriers. The usual implementation of the REM is performed on local computer clusters (or parallel processors) where the different replicas must be run synchronously. Here, we present serial replica exchange (SREM), a method that is equivalent to the standard REM in terms of efficiency yet runs asynchronously on a distributed network of computers. A second advantage is the method's greatly enhanced fault tolerance, which enables the study of biological systems on worldwide distributed computing environments, such as Folding@Home. For proof of concept, we apply the SREM to a single alanine dipeptide molecule in explicit water. We show that the SREM reproduces the thermodynamic and structural properties determined by the REM.
authors.affiliation: Department of Chemistry and Center for Biomolecular Simulation, Columbia University, New York, New York 10027, USA.
authors.forename: Morten
authors.initials: M
authors.lastname: Hagen
authors.forename: Byungchan
authors.initials: B
authors.lastname: Kim
authors.forename: Pu
authors.initials: P
authors.lastname: Liu
authors.forename: Richard A
authors.initials: RA
authors.lastname: Friesner
authors.forename: B J
authors.initials: BJ
authors.lastname: Berne
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D004151:Dipeptides / Q000737:chemistry; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D012996:Solutions / Q000737:chemistry; D013816:Thermodynamics; D013997:Time Factors; D014867:Water / Q000737:chemistry
chemical_list: D004151:Dipeptides; D011506:Proteins; D012996:Solutions; D014867:Water; C002956:alanylalanine