Generalized-ensemble simulations in protein science

Yoshiharu Mori, Ayori Mitsutake, Yuko Okamoto

研究成果: Chapter

抄録

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.

本文言語English
ホスト出版物のタイトルMolecular Dynamics of Nanobiostructures
出版社Nova Science Publishers, Inc.
ページ63-84
ページ数22
ISBN(印刷版)9781613243206
出版ステータスPublished - 2013 1 1

ASJC Scopus subject areas

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

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