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

Hiroshi Yamashita, Shigeru Endo, Hiroshi Wako, Akinori Kidera

研究成果: Article査読

18 被引用数 (Scopus)

抄録

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.

本文言語English
ページ(範囲)382-386
ページ数5
ジャーナルChemical Physics Letters
342
3-4
DOI
出版ステータスPublished - 2001 7 13

ASJC Scopus subject areas

  • 物理学および天文学(全般)
  • 物理化学および理論化学

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