### 抄録

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 multiplehistogram 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 generalizedensemble 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.

元の言語 | English |
---|---|

ページ（範囲） | 96-123 |

ページ数 | 28 |

ジャーナル | Biopolymers - Peptide Science Section |

巻 | 60 |

発行部数 | 2 |

DOI | |

出版物ステータス | Published - 2001 |

外部発表 | Yes |

### Fingerprint

### ASJC Scopus subject areas

- Biochemistry, Genetics and Molecular Biology(all)
- Biochemistry
- Biophysics

### これを引用

*Biopolymers - Peptide Science Section*,

*60*(2), 96-123. https://doi.org/10.1002/1097-0282(2001)60:2<96::AID-BIP1007>3.0.CO;2-F

**Generalized-ensemble algorithms for molecular simulations of biopolymers.** / Mitsutake, Ayori; Sugita, Yuji; Okamoto, Yuko.

研究成果: Article

*Biopolymers - Peptide Science Section*, 巻. 60, 番号 2, pp. 96-123. https://doi.org/10.1002/1097-0282(2001)60:2<96::AID-BIP1007>3.0.CO;2-F

}

TY - JOUR

T1 - Generalized-ensemble algorithms for molecular simulations of biopolymers

AU - Mitsutake, Ayori

AU - Sugita, Yuji

AU - Okamoto, Yuko

PY - 2001

Y1 - 2001

N2 - 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 multiplehistogram 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 generalizedensemble 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.

AB - 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 multiplehistogram 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 generalizedensemble 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.

KW - Generalized-ensemble algorithm

KW - Multicanonical algorithm

KW - Parallel tempering

KW - Protein folding

KW - Replica-exchange method

KW - Simulated tempering

UR - http://www.scopus.com/inward/record.url?scp=0034864528&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0034864528&partnerID=8YFLogxK

U2 - 10.1002/1097-0282(2001)60:2<96::AID-BIP1007>3.0.CO;2-F

DO - 10.1002/1097-0282(2001)60:2<96::AID-BIP1007>3.0.CO;2-F

M3 - Article

C2 - 11455545

AN - SCOPUS:0034864528

VL - 60

SP - 96

EP - 123

JO - Biopolymers

JF - Biopolymers

SN - 0006-3525

IS - 2

ER -