Generalized-ensemble algorithms for molecular simulations of biopolymers

Ayori Mitsutake, Yuji Sugita, Yuko Okamoto

Research output: Contribution to journalArticle

626 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)96-123
Number of pages28
JournalBiopolymers - Peptide Science Section
Volume60
Issue number2
DOIs
Publication statusPublished - 2001
Externally publishedYes

Fingerprint

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

Keywords

  • Generalized-ensemble algorithm
  • Multicanonical algorithm
  • Parallel tempering
  • Protein folding
  • Replica-exchange method
  • Simulated tempering

ASJC Scopus subject areas

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

Cite this

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

In: Biopolymers - Peptide Science Section, Vol. 60, No. 2, 2001, p. 96-123.

Research output: Contribution to journalArticle

Mitsutake, Ayori ; Sugita, Yuji ; Okamoto, Yuko. / Generalized-ensemble algorithms for molecular simulations of biopolymers. In: Biopolymers - Peptide Science Section. 2001 ; Vol. 60, No. 2. pp. 96-123.
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