Multidimensional generalized-ensemble algorithms for complex systems

Ayori Mitsutake, Yuko Okamoto

Research output: Contribution to journalArticle

50 Citations (Scopus)

Abstract

We give general formulations of the multidimensional multicanonical algorithm, simulated tempering, and replica-exchange method. We generalize the original potential energy function E0 by adding any physical quantity V of interest as a new energy term. These multidimensional generalized-ensemble algorithms then perform a random walk not only in E0 space but also in V space. Among the three algorithms, the replica-exchange method is the easiest to perform because the weight factor is just a product of regular Boltzmann-like factors, while the weight factors for the multicanonical algorithm and simulated tempering are not a priori known. We give a simple procedure for obtaining the weight factors for these two latter algorithms, which uses a short replica-exchange simulation and the multiple-histogram reweighting techniques. As an example of applications of these algorithms, we have performed a two-dimensional replica-exchange simulation and a two-dimensional simulated-tempering simulation using an α -helical peptide system. From these simulations, we study the helix-coil transitions of the peptide in gas phase and in aqueous solution.

Original languageEnglish
Article number214105
JournalJournal of Chemical Physics
Volume130
Issue number21
DOIs
Publication statusPublished - 2009

Fingerprint

complex systems
Large scale systems
weight (mass)
replicas
tempering
Tempering
Weights and Measures
peptides
simulation
Potential energy functions
Peptides
random walk
histograms
helices
coils
Gases
potential energy
vapor phases
aqueous solutions
formulations

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry
  • Medicine(all)

Cite this

Multidimensional generalized-ensemble algorithms for complex systems. / Mitsutake, Ayori; Okamoto, Yuko.

In: Journal of Chemical Physics, Vol. 130, No. 21, 214105, 2009.

Research output: Contribution to journalArticle

Mitsutake, Ayori ; Okamoto, Yuko. / Multidimensional generalized-ensemble algorithms for complex systems. In: Journal of Chemical Physics. 2009 ; Vol. 130, No. 21.
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