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

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-va...

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Bibliographic Details
Published inChemical physics letters Vol. 342; no. 3; pp. 382 - 386
Main Authors Yamashita, Hiroshi, Endo, Shigeru, Wako, Hiroshi, Kidera, Akinori
Format Journal Article
LanguageEnglish
Published Amsterdam Elsevier B.V 13.07.2001
Elsevier Science
Subjects
Biological and medical sciences
Fundamental and applied biological sciences. Psychology
General aspects
Molecular biophysics
Theory and modeling; computer simulation
Monte Carlo method
Numerical simulation
Molecular structure
Sampling
Protein
Molecular dynamics method
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Summary: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.
ISSN:0009-2614
1873-4448
DOI:10.1016/S0009-2614(01)00613-3