TY - CHAP

T1 - Generalized-ensemble algorithms for protein folding simulations

AU - Sugita, Yuji

AU - Mitsutake, Ayori

AU - Okamoto, Yuko

N1 - Copyright:
Copyright 2008 Elsevier B.V., All rights reserved.

PY - 2008

Y1 - 2008

N2 - 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.

AB - 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.

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U2 - 10.1007/978-3-540-74029-2_14

DO - 10.1007/978-3-540-74029-2_14

M3 - Chapter

AN - SCOPUS:37549026242

SN - 9783540740254

T3 - Lecture Notes in Physics

SP - 369

EP - 407

BT - Rugged Free Energy Landscapes

A2 - Janke, Wolfhard

ER -