Generalized-ensemble simulations of spin systems and protein systems

Takehiro Nagasima, Yuji Sugita, Ayori Mitsutake, Yuko Okamoto

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

In complex systems such as spin systems and protein systems, conventional simulations in the canonical ensemble will get trapped in states of energy local minima. We employ the generalized-ensemble algorithms in order to overcome this multiple-minima problem. Three well-known generalized-ensemble algorithms, namely, multicanonical algorithm, simulated tempering, and replica-exchange method, are described. We then present three new generalized-ensemble algorithms based on the combinations of the three methods. Effectiveness of the new methods are tested with a Potts model and protein systems.

Original languageEnglish
Pages (from-to)69-76
Number of pages8
JournalComputer Physics Communications
Volume146
Issue number1
DOIs
Publication statusPublished - 2002 Jun 15

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proteins
Proteins
simulation
Potts model
tempering
systems simulation
Tempering
complex systems
replicas
Large scale systems
energy

Keywords

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

ASJC Scopus subject areas

  • Computer Science Applications
  • Physics and Astronomy(all)

Cite this

Generalized-ensemble simulations of spin systems and protein systems. / Nagasima, Takehiro; Sugita, Yuji; Mitsutake, Ayori; Okamoto, Yuko.

In: Computer Physics Communications, Vol. 146, No. 1, 15.06.2002, p. 69-76.

Research output: Contribution to journalArticle

Nagasima, Takehiro ; Sugita, Yuji ; Mitsutake, Ayori ; Okamoto, Yuko. / Generalized-ensemble simulations of spin systems and protein systems. In: Computer Physics Communications. 2002 ; Vol. 146, No. 1. pp. 69-76.
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