Sampling efficiency of molecular dynamics and Monte Carlo method in protein simulation

Hiroshi Yamashita, Shigeru Endo, Hiroshi Wako, Akinori Kidera

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18 Citations (Scopus)

Abstract

Molecular dynamics (MD) and Monte Carlo (MC) method were compared in terms of the sampling efficiency in protein simulations. In the comparison, both methods use torsion angles as the degrees of freedom and the same force field, ECEPP/2. The MC method used here is the force-bias scaled-collective-variable Monte Carlo (SCV MC) [A. Kidera, Int. J. Quant. Chem. 75 (1999) 207], which corresponds to a finite step size extension to Brownian dynamics. It is shown that MD has about 1.5 times larger sampling efficiency. This difference is attributed to the inertia force term in MD, which does not exist in MC.

Original languageEnglish
Pages (from-to)382-386
Number of pages5
JournalChemical Physics Letters
Volume342
Issue number3-4
DOIs
Publication statusPublished - 2001 Jul 13

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ASJC Scopus subject areas

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

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