Generalized-ensemble algorithms for molecular simulations of biopolymers.
In complex systems with many degrees of freedom such as peptides and proteins, there exists a huge number of local-minimum-energy states. Conventional simulations in the canonical ensemble are of little use, because they tend to get trapped in states of these energy local minima. A simulation in generalized ensemble performs a random walk in potential energy space and can overcome this difficulty. 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 uses of the generalized-ensemble algorithms in biomolecular systems. 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 three new generalized-ensemble algorithms that combine the merits of the above methods. The effectiveness of the methods for molecular simulations in the protein folding problem is tested with short peptide systems.
Mitsutake
A
A
Department of Theoretical Studies, Institute for Molecular Science, Okazaki, Aichi, Japan.
Sugita
Y
Y
Okamoto
Y
Y
D000465:Algorithms; D000595:Amino Acid Sequence; D001704:Biopolymers / Q000737:chemistry*; D003198:Computer Simulation; D008958:Models, Molecular; D009010:Monte Carlo Method; D009842:Oligopeptides / Q000737:chemistry; D011487:Protein Conformation; D012996:Solutions; D013816:Thermodynamics; D014867:Water
D001704:Biopolymers; D009842:Oligopeptides; D012996:Solutions; D014867:Water