title: On the use of mass scaling for stable and efficient simulated tempering with molecular dynamics.
abstract: Simulated tempering (ST) is a generalized-ensemble algorithm that employs trajectories exploring a range of temperatures to effectively sample rugged energy landscapes. When implemented using the molecular dynamics method, ST can require the use of short time steps for ensuring the stability of trajectories at high temperatures. To address this shortcoming, a mass-scaling ST (MSST) method is presented in which the particle mass is scaled in proportion to the temperature. Mass scaling in the MSST method leads to velocity distributions that are independent of temperature and eliminates the need for velocity scaling after the accepted temperature updates that are required in conventional ST simulations. The homogeneity in time scales with changing temperature improves the stability of simulations and allows for the use of longer time steps at high temperatures. As a result, the MSST is found to be more efficient than the standard ST method, particularly for cases in which a large temperature range is employed. © 2016 Wiley Periodicals, Inc.
authors.affiliation: Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan.
authors.forename: Tetsuro
authors.initials: T
authors.lastname: Nagai
authors.affiliation: Department of Chemistry, Boston University, Boston, Massachusetts, 02215.
authors.forename: George A
authors.initials: GA
authors.lastname: Pantelopulos
authors.affiliation: Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan.
authors.forename: Takuya
authors.initials: T
authors.lastname: Takahashi
authors.affiliation: Department of Chemistry, Boston University, Boston, Massachusetts, 02215.
authors.forename: John E
authors.initials: JE
authors.lastname: Straub
keywords: Nosé-Hoover thermostat; generalized-ensemble algorithm; mass scaling; molecular dynamics; simulated tempering