Generalized-Ensemble Algorithms for Protein Folding Simulations

Details Generalized-Ensemble Algorithms for Protein Folding Simulations Generalized-Ensemble Algorithms for Protein Folding Simulations

2007-07-23

arxiv.org/abs/0707.3382v1

Physics

Condensed Matter

Statistical Mechanics

37 pages, (LaTeX2e), 5 figures

Scientific paper

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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