title: Improving Convergence of Replica-Exchange Simulations through Coupling to a High-Temperature Structure Reservoir.
abstract: Parallel tempering or replica-exchange molecular dynamics (REMD) significantly increases the efficiency of conformational sampling for complex molecular systems. However, obtaining converged data with REMD remains challenging, especially for large systems with complex topologies. We propose a new variant to REMD where the replicas are also permitted to exchange with an ensemble of structures that have been generated in advance using high-temperature MD simulations, similar in spirit to J-walking methods. We tested this approach on two non-trivial model systems, a β-hairpin and a 3-stranded β-sheet and compared the results to those obtained from very long (>100 ns) standard REMD simulations. The resulting ensembles were indistinguishable, including relative populations of different conformations on the unfolded state. The use of the reservoir is shown to significantly reduce the time required for convergence.
authors.affiliation: Department of Chemistry and Center for Structural Biology, Stony Brook University, Stony Brook, New York 11794, and Computational Science Center, Brookhaven National Laboratory, Upton, New York 11973.
authors.forename: Asim
authors.initials: A
authors.lastname: Okur
authors.affiliation: Department of Chemistry and Center for Structural Biology, Stony Brook University, Stony Brook, New York 11794, and Computational Science Center, Brookhaven National Laboratory, Upton, New York 11973.
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Roe
authors.affiliation: Department of Chemistry and Center for Structural Biology, Stony Brook University, Stony Brook, New York 11794, and Computational Science Center, Brookhaven National Laboratory, Upton, New York 11973.
authors.forename: Guanglei
authors.initials: G
authors.lastname: Cui
authors.affiliation: Department of Chemistry and Center for Structural Biology, Stony Brook University, Stony Brook, New York 11794, and Computational Science Center, Brookhaven National Laboratory, Upton, New York 11973.
authors.forename: Viktor
authors.initials: V
authors.lastname: Hornak
authors.affiliation: Department of Chemistry and Center for Structural Biology, Stony Brook University, Stony Brook, New York 11794, and Computational Science Center, Brookhaven National Laboratory, Upton, New York 11973.
authors.forename: Carlos
authors.initials: C
authors.lastname: Simmerling