Determination of multicanonical weight based on a stochastic model of sampling dynamics

Jae Gil Kim¹, Yoshifumi Fukunishi, Akinori Kidera

¹Japan Biological Information Research Center (JBIRC), Japan Biological Informatics Consortium (JBIC), Aomi 2-41-6, Koto-ku, Tokyo, 135-0064, Japan. jgkim@jbirc.aist.go.jp

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics

|October 4, 2003

Abstract:

Based on the stochastic interpretation of the sampling process modeled by a Langevin equation, we present an effective iteration scheme to determine the weight in multicanonical molecular dynamics. Our method enables an automatic determination of the weight producing a uniform energy sampling via an iterative cancellation of the deterministic force in a Langevin equation. The deterministic force has been calculated from the energy trajectory by identifying the moments of the transition probability of a Fokker-Planck equation associated with a Langevin equation. The intimate relationship between the sampling process and the stochastic dynamics has been verified by applying the iteration scheme to a helix-coil transition of the 8-polyalanine system in a gas phase.

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Abstract:

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