Generalized-ensemble algorithms for protein folding simulations

Yuji Sugita, Ayori Mitsutake, Yuko Okamoto

研究成果: Chapter

10 被引用数 (Scopus)

抄録

Conventional simulations of complex systems in the canonical ensemble suffer from the quasi-ergodicity problem. A simulation in generalized ensemble overcomes this difficulty by performing a random walk in potential energy space and other parameter space. From only one simulation run, one can obtain canonical-ensemble averages of physical quantities as functions of temperature by the single-histogram and/or multiple-histogram reweighting techniques. In this article, we review the generalized-ensemble algorithms. Three well-known methods, namely multicanonical algorithm, simulated tempering, and replica-exchange method, are described first. Both Monte Carlo and molecular dynamics versions of the algorithms are given. We then present further extensions of the above three methods.

本文言語English
ホスト出版物のタイトルRugged Free Energy Landscapes
ホスト出版物のサブタイトルCommon Computational Approaches to Spin Glasses, Structural Glasses and Biological Macromolecules
編集者Wolfhard Janke
ページ369-407
ページ数39
DOI
出版ステータスPublished - 2008
外部発表はい

出版物シリーズ

名前Lecture Notes in Physics
736
ISSN(印刷版)0075-8450

ASJC Scopus subject areas

  • 物理学および天文学(その他)

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