Multi-dimensional multicanonical algorithm, simulated tempering, replica-exchange method, and all that

Ayori Mitsutake, Yoshiharu Mori, Yuko Okamoto

Research output: Chapter in Book/Report/Conference proceedingConference contribution

5 Citations (Scopus)

Abstract

We discuss multi-dimensional generalizations of 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 with a coupling constant λ. We then perform a multi-dimensional multicanonical simulation where a random walk in E 0 and V space is realized. We can alternately perform a multi-dimensional simulated-tempering simulation where a random walk in temperature T and parameter λ is realized. The results of the multi-dimensional replica-exchange simulations can be used to determine the weight factors for these multi-dimensional multicanonical and simulated tempering simulations. Two examples of the above methods are presented for biomoleculr systems where the parameter λ corresponds to the solvation parameter and the pressure. In the former, a random walk in the conformational energy and solvation free energy is performed, and in the latter, a random walk in the potential energy and volume is realized.

Original languageEnglish
Title of host publicationPhysics Procedia
Pages89-105
Number of pages17
Volume4
DOIs
Publication statusPublished - 2010
Event23rd Annual Workshop on Recent Developments in Computer Simulation Studies in Condensed Matter Physics - Athens, GA, United States
Duration: 2010 Feb 222010 Feb 26

Other

Other23rd Annual Workshop on Recent Developments in Computer Simulation Studies in Condensed Matter Physics
CountryUnited States
CityAthens, GA
Period10/2/2210/2/26

Fingerprint

tempering
replicas
random walk
solvation
simulation
potential energy
weight (mass)
free energy
energy
temperature

Keywords

  • Generalized-ensemble algorithms
  • Molecular dynamics
  • Mont Carlo
  • Multicanonical algorithm
  • Parallel tempering
  • Replica-exchange method
  • Simulated tempering

ASJC Scopus subject areas

  • Physics and Astronomy(all)

Cite this

Multi-dimensional multicanonical algorithm, simulated tempering, replica-exchange method, and all that. / Mitsutake, Ayori; Mori, Yoshiharu; Okamoto, Yuko.

Physics Procedia. Vol. 4 2010. p. 89-105.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Mitsutake, A, Mori, Y & Okamoto, Y 2010, Multi-dimensional multicanonical algorithm, simulated tempering, replica-exchange method, and all that. in Physics Procedia. vol. 4, pp. 89-105, 23rd Annual Workshop on Recent Developments in Computer Simulation Studies in Condensed Matter Physics, Athens, GA, United States, 10/2/22. https://doi.org/10.1016/j.phpro.2010.08.012
Mitsutake, Ayori ; Mori, Yoshiharu ; Okamoto, Yuko. / Multi-dimensional multicanonical algorithm, simulated tempering, replica-exchange method, and all that. Physics Procedia. Vol. 4 2010. pp. 89-105
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