Generalized-ensemble algorithms for protein folding simulations

Yuji Sugita, Ayori Mitsutake, Yuko Okamoto

Research output: Chapter in Book/Report/Conference proceedingChapter

10 Citations (Scopus)

Abstract

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.

Original languageEnglish
Title of host publicationRugged Free Energy Landscapes
Subtitle of host publicationCommon Computational Approaches to Spin Glasses, Structural Glasses and Biological Macromolecules
EditorsWolfhard Janke
Pages369-407
Number of pages39
DOIs
Publication statusPublished - 2008 Jan 4

Publication series

NameLecture Notes in Physics
Volume736
ISSN (Print)0075-8450

ASJC Scopus subject areas

  • Physics and Astronomy (miscellaneous)

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    Sugita, Y., Mitsutake, A., & Okamoto, Y. (2008). Generalized-ensemble algorithms for protein folding simulations. In W. Janke (Ed.), Rugged Free Energy Landscapes: Common Computational Approaches to Spin Glasses, Structural Glasses and Biological Macromolecules (pp. 369-407). (Lecture Notes in Physics; Vol. 736). https://doi.org/10.1007/978-3-540-74029-2_14