TY - CHAP
T1 - Generalized-ensemble algorithms for protein folding simulations
AU - Sugita, Yuji
AU - Mitsutake, Ayori
AU - Okamoto, Yuko
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 -