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

Fingerprint

Tempering
Potential energy
Peptides
proteins
Proteins
simulation
Temperature
tempering
replicas
random walk
histograms
encounters
peptides
potential energy
temperature
energy

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)

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..

Generalized-ensemble simulations in protein science. / Mori, Yoshiharu; Mitsutake, Ayori; Okamoto, Yuko.

Molecular Dynamics of Nanobiostructures. Nova Science Publishers, Inc., 2013. p. 63-84.

Research output: Chapter in Book/Report/Conference proceedingChapter

Mori, Y, Mitsutake, A & Okamoto, Y 2013, Generalized-ensemble simulations in protein science. in Molecular Dynamics of Nanobiostructures. Nova Science Publishers, Inc., pp. 63-84.
Mori Y, Mitsutake A, Okamoto Y. Generalized-ensemble simulations in protein science. In Molecular Dynamics of Nanobiostructures. Nova Science Publishers, Inc. 2013. p. 63-84
Mori, Yoshiharu ; Mitsutake, Ayori ; Okamoto, Yuko. / Generalized-ensemble simulations in protein science. Molecular Dynamics of Nanobiostructures. Nova Science Publishers, Inc., 2013. pp. 63-84
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