Generalized-ensemble simulations in protein science

Yoshiharu Mori, Ayori Mitsutake, Yuko Okamoto

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

In simulations in materials and biological sciences, one encounters with a great difficulty that conventional simulations will tend to get trapped in states of energy local minima. A simulation in generalized ensemble performs a random walk in potential energy space and can overcome this difficulty. From only one simulation run, one can obtain canonical-ensemble averages of physical quantities as functions of temperature by the histogram reweighting techniques. We review thegeneralized-ensemble algorithms. The multidimensional extensions of the replica-exchange method and simulated tempering are presented. The effectiveness of the methods is tested with short peptide and protein systems.

Original languageEnglish
Title of host publicationMolecular Dynamics of Nanobiostructures
PublisherNova Science Publishers, Inc.
Pages63-84
Number of pages22
ISBN (Print)9781613243206
Publication statusPublished - 2013 Jan 1

Keywords

  • Generalized-ensemble algorithm
  • Molecular dynamics
  • Monte carlo
  • Replica-exchange method
  • Simulated tempering

ASJC Scopus subject areas

  • Chemical Engineering(all)
  • Physics and Astronomy(all)
  • Chemistry(all)

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  • Cite this

    Mori, Y., Mitsutake, A., & Okamoto, Y. (2013). Generalized-ensemble simulations in protein science. In Molecular Dynamics of Nanobiostructures (pp. 63-84). Nova Science Publishers, Inc..