title: Replica state exchange metadynamics for improving the convergence of free energy estimates.
abstract: Metadynamics (MTD) is a powerful enhanced sampling method for systems with rugged energy landscapes. It constructs a bias potential in a predefined collective variable (CV) space to overcome barriers between metastable states. In bias-exchange MTD (BE-MTD), multiple replicas approximate the CV space by exchanging bias potentials (replica conditions) with the Metropolis-Hastings (MH) algorithm. We demonstrate that the replica-exchange rates and the convergence of free energy estimates of BE-MTD are improved by introducing the infinite swapping (IS) or the Suwa-Todo (ST) algorithms. Conceptually, IS and ST perform transitions in a replica state space rather than exchanges in a replica condition space. To emphasize this, the proposed scheme is called the replica state exchange MTD (RSE-MTD). Benchmarks were performed with alanine polypeptides in vacuum and water. For the systems tested in this work, there is no significant performance difference between IS and ST.
authors.affiliation: RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.|RIKEN Advance Institute for Computational Science, 7-1-26 Minatojimaminamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.
authors.forename: Raimondas
authors.initials: R
authors.lastname: Galvelis
authors.affiliation: RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.|RIKEN Advance Institute for Computational Science, 7-1-26 Minatojimaminamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.|RIKEN iTHES, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.|RIKEN Quantitative Biology Center, IMDA 6F, 1-6-5 Minatojimaminamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.
authors.forename: Yuji
authors.initials: Y
authors.lastname: Sugita
mesh_terms: D000409:Alanine / Q000737:chemistry*; D000465:Algorithms; D056004:Molecular Dynamics Simulation; D009010:Monte Carlo Method; D010455:Peptides / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D010455:Peptides; D000409:Alanine
keywords: Metropolis-Hastings algorithm; Suwa-Todo algorithm; enhanced sampling; free energy; infinite swapping; metadynamics