Effective sampling algorithms and analysis method for biomolecular simulations

Ayori Mitsutake

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

Abstract

Conventional simulations of complex systems, which have many degrees of freedom, are hampered by multiple-minima problem. One way to overcome the multiple-minima problem is to perform a simulation in a generalized ensemble where each state is weighted by an artificial, non-Boltzmann weight factor so that a random walk in potential energy space may be realized. Three of well-known generalized-ensemble algorithms are multicanonical, simulated-tempering, and replica exchange method. In previous works, the methods combined with simulated-tempering and replica-exchange method, the one-dimensional replica-exchange simulated-tempering and simulated-tempering replica-exchange method, were developed. For the former method, the weight factor of the one-dimensional simulated-tempering is determined by a short replica-exchange simulation and multiple histogram reweighting techniques. For the latter method, the production run is a replica-exchange simulation with a few replicas not in the canonical ensembles but in the simulated-tempering ensembles. In this article, the general formulation of the multidimensional replica-exchange simulated-tempering and simulated-tempering replica exchange method is reviewed.

Original languageEnglish
Title of host publication4th International Symposium on Slow Dynamics in Complex Systems
Subtitle of host publicationKeep Going Tohoku
PublisherAmerican Institute of Physics Inc.
Pages598-601
Number of pages4
ISBN (Print)9780735411418
DOIs
Publication statusPublished - 2013 Jan 1
Event4th International Symposium on Slow Dynamics in Complex Systems: Keep Going Tohoku - Sendai, Japan
Duration: 2012 Dec 22012 Dec 7

Publication series

NameAIP Conference Proceedings
Volume1518
ISSN (Print)0094-243X
ISSN (Electronic)1551-7616

Other

Other4th International Symposium on Slow Dynamics in Complex Systems: Keep Going Tohoku
CountryJapan
CitySendai
Period12/12/212/12/7

Keywords

  • Generalized ensemble
  • biomolecular
  • simulation

ASJC Scopus subject areas

  • Physics and Astronomy(all)

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  • Cite this

    Mitsutake, A. (2013). Effective sampling algorithms and analysis method for biomolecular simulations. In 4th International Symposium on Slow Dynamics in Complex Systems: Keep Going Tohoku (pp. 598-601). (AIP Conference Proceedings; Vol. 1518). American Institute of Physics Inc.. https://doi.org/10.1063/1.4794640