TY - JOUR
T1 - Sampling efficiency of molecular dynamics and Monte Carlo method in protein simulation
AU - Yamashita, Hiroshi
AU - Endo, Shigeru
AU - Wako, Hiroshi
AU - Kidera, Akinori
N1 - Funding Information:
The computations were done in the Computer Center of Institute for Molecular Science, Center for Promotion of Computational Science and Engineering of JAERI. This work was supported by the Grant-in-Aid for Scientific Research from MEXT to A.K.
PY - 2001/7/13
Y1 - 2001/7/13
N2 - 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.
AB - 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.
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U2 - 10.1016/S0009-2614(01)00613-3
DO - 10.1016/S0009-2614(01)00613-3
M3 - Article
AN - SCOPUS:0042877270
SN - 0009-2614
VL - 342
SP - 382
EP - 386
JO - Chemical Physics Letters
JF - Chemical Physics Letters
IS - 3-4
ER -