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

Hiroshi Yamashita, Shigeru Endo, Hiroshi Wako, Akinori Kidera

Research output: Contribution to journalArticle

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

Fingerprint

Monte Carlo method
Molecular dynamics
Monte Carlo methods
sampling
molecular dynamics
Sampling
proteins
Proteins
simulation
Degrees of freedom (mechanics)
inertia
Torsional stress
field theory (physics)
torsion
degrees of freedom

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Spectroscopy
  • Atomic and Molecular Physics, and Optics

Cite this

Sampling efficiency of molecular dynamics and Monte Carlo method in protein simulation. / Yamashita, Hiroshi; Endo, Shigeru; Wako, Hiroshi; Kidera, Akinori.

In: Chemical Physics Letters, Vol. 342, No. 3-4, 13.07.2001, p. 382-386.

Research output: Contribution to journalArticle

Yamashita, Hiroshi ; Endo, Shigeru ; Wako, Hiroshi ; Kidera, Akinori. / Sampling efficiency of molecular dynamics and Monte Carlo method in protein simulation. In: Chemical Physics Letters. 2001 ; Vol. 342, No. 3-4. pp. 382-386.
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