Literature DB >> 26466561

Simulated tempering based on global balance or detailed balance conditions: Suwa-Todo, heat bath, and Metropolis algorithms.

Yoshiharu Mori1, Hisashi Okumura2,3.   

Abstract

Simulated tempering (ST) is a useful method to enhance sampling of molecular simulations. When ST is used, the Metropolis algorithm, which satisfies the detailed balance condition, is usually applied to calculate the transition probability. Recently, an alternative method that satisfies the global balance condition instead of the detailed balance condition has been proposed by Suwa and Todo. In this study, ST method with the Suwa-Todo algorithm is proposed. Molecular dynamics simulations with ST are performed with three algorithms (the Metropolis, heat bath, and Suwa-Todo algorithms) to calculate the transition probability. Among the three algorithms, the Suwa-Todo algorithm yields the highest acceptance ratio and the shortest autocorrelation time. These suggest that sampling by a ST simulation with the Suwa-Todo algorithm is most efficient. In addition, because the acceptance ratio of the Suwa-Todo algorithm is higher than that of the Metropolis algorithm, the number of temperature states can be reduced by 25% for the Suwa-Todo algorithm when compared with the Metropolis algorithm.
© 2015 Wiley Periodicals, Inc.

Keywords:  correlation; generalized-ensemble algorithm; molecular dynamics; molecular simulation; random walk

Mesh:

Year:  2015        PMID: 26466561     DOI: 10.1002/jcc.24213

Source DB:  PubMed          Journal:  J Comput Chem        ISSN: 0192-8651            Impact factor:   3.376


  4 in total

Review 1.  Molecular simulations by generalized-ensemble algorithms in isothermal-isobaric ensemble.

Authors:  Masataka Yamauchi; Yoshiharu Mori; Hisashi Okumura
Journal:  Biophys Rev       Date:  2019-05-21

Review 2.  All-Atom Molecular Dynamics Simulation Methods for the Aggregation of Protein and Peptides: Replica Exchange/Permutation and Nonequilibrium Simulations.

Authors:  Satoru G Itoh; Hisashi Okumura
Journal:  Methods Mol Biol       Date:  2022

Review 3.  Molecular Dynamics Simulation Studies on the Aggregation of Amyloid-β Peptides and Their Disaggregation by Ultrasonic Wave and Infrared Laser Irradiation.

Authors:  Hisashi Okumura; Satoru G Itoh
Journal:  Molecules       Date:  2022-04-12       Impact factor: 4.927

Review 4.  Promotion and Inhibition of Amyloid-β Peptide Aggregation: Molecular Dynamics Studies.

Authors:  Satoru G Itoh; Hisashi Okumura
Journal:  Int J Mol Sci       Date:  2021-02-13       Impact factor: 5.923

  4 in total

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