Generalized-ensemble algorithms for molecular simulations of biopolymers

Ayori Mitsutake, Yuji Sugita, Yuko Okamoto

研究成果: Article

628 引用 (Scopus)

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
60
発行部数2
DOI
出版物ステータスPublished - 2001
外部発表Yes

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Biopolymers
Peptides
Protein folding
Protein Folding
Tempering
Molecular Dynamics Simulation
Potential energy
Electron energy levels
Molecular dynamics
Large scale systems
Proteins
Temperature

ASJC Scopus subject areas

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

これを引用

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

:: Biopolymers - Peptide Science Section, 巻 60, 番号 2, 2001, p. 96-123.

研究成果: Article

Mitsutake, Ayori ; Sugita, Yuji ; Okamoto, Yuko. / Generalized-ensemble algorithms for molecular simulations of biopolymers. :: Biopolymers - Peptide Science Section. 2001 ; 巻 60, 番号 2. pp. 96-123.
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