On the use of mass scaling for stable and efficient simulated tempering with molecular dynamics. Issue 21 (24th June 2016)

• Record Type: Journal Article
• Authors: Nagai, Tetsuro; Pantelopulos, George A.; Takahashi, Takuya; Straub, John E.
• Is Part Of: Journal of computational chemistry. Volume 37:Issue 21(2016)
• Page Start: 2017
• Page End: 2028
• Publication Date: 2016-06-24
• Subjects: generalized‐ensemble algorithm -- simulated tempering -- mass scaling -- Nosé–Hoover thermostat -- molecular dynamics; Chemistry -- Data processing -- Periodicals; 542.85
• DOI: 10.1002/jcc.24430
• Languages: English
• ISSNs: 0192-8651

Abstract

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. Abstract : Simulated tempering (ST) is a commonly practiced generalized‐ensemble algorithm that combines simulations at multiple temperatures. To perform efficient and stable ST simulation using molecular dynamics, the mass‐scaling ST method is presented. The proper mass scaling employed in the new method makes the velocity distributions independent of temperature. This homogeneity enables simple temperature updates and makes the tempering simulation stable at high temperatures. The MSST method is applied to the folding of the Trpcage peptide over a wide range of temperature to demonstrate the gain in numerical stability.