Literature DB >> 16381079

Multibaric-multithermal ensemble molecular dynamics simulations.

Hisashi Okumura1, Yuko Okamoto.   

Abstract

We present new generalized-ensemble molecular dynamics simulation algorithms, which we refer to as the multibaric-multithermal molecular dynamics. We describe three algorithms based on (1) the Nosé thermostat and the Andersen barostat, (2) the Nosé-Poincaré thermostat and the Andersen barostat, and (3) the Gaussian thermostat and the Andersen barostat. The multibaric-multithermal simulations perform random walks widely both in the potential-energy space and in the volume space. Therefore, one can calculate isobaric-isothermal ensemble averages in wide ranges of temperature and pressure from only one simulation run. We test the effectiveness of the multibaric-multithermal algorithm by applying it to a Lennard-Jones 12-6 potential system.

Year:  2006        PMID: 16381079     DOI: 10.1002/jcc.20351

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


  7 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

3.  Molecular dynamics simulations of amyloid-β peptides in heterogeneous environments.

Authors:  Yuhei Tachi; Satoru G Itoh; Hisashi Okumura
Journal:  Biophys Physicobiol       Date:  2022-04-02

Review 4.  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

5.  Conformational populations of ligand-sized molecules by replica exchange molecular dynamics and temperature reweighting.

Authors:  Hisashi Okumura; Emilio Gallicchio; Ronald M Levy
Journal:  J Comput Chem       Date:  2010-05       Impact factor: 3.376

6.  Theoretical analysis on thermodynamic stability of chignolin.

Authors:  Tomonari Sumi; Kenichiro Koga
Journal:  Sci Rep       Date:  2019-03-26       Impact factor: 4.379

Review 7.  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

  7 in total

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