A new generalized-ensemble algorithm: multicanonical-multioverlap algorithm

被引:13
作者
Itoh, S. G. [1 ]
Okamoto, Y.
机构
[1] Nagoya Univ, Sch Sci, Dept Phys, Nagoya, Aichi 4648602, Japan
[2] Inst Mol Sci, Res Ctr Computat Sci, Okazaki, Aichi 444, Japan
关键词
molecular dynamics simulation; generalized-ensemble algorithm; protein folding; transition state;
D O I
10.1080/08927020601075345
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
We introduce a new generalized-ensemble algorithm, which we refer to as the multicanonical-multioverlap algorithm. By utilizing a non-Boltzmann weight factor, this method realizes a random walk in the multi-dimensional, energy-overlap space and explores widely in the configurational space including specific configurations, where the overlap of a configuration with respect to a reference state is a measure for structural similarity. We apply the multicanonical-multioverlap molecular dynamics (MD) method to a penta peptide, Met-enkephalin, in vacuum as a test system. We also apply the multicanonical and multioverlap MD methods to this system for the purpose of comparisons. We see that the multicanonical-multioverlap MD method realizes effective sampling in the configurational space including specific configurations more than the other two methods.
引用
收藏
页码:83 / 89
页数:7
相关论文
共 30 条
[1]  
[Anonymous], LECT NOTES COMPUTATI
[2]   Algorithmic aspects of multicanonical simulations [J].
Berg, BA .
NUCLEAR PHYSICS B-PROCEEDINGS SUPPLEMENTS, 1998, 63 :982-984
[3]   NEW APPROACH TO SPIN-GLASS SIMULATIONS [J].
BERG, BA ;
CELIK, T .
PHYSICAL REVIEW LETTERS, 1992, 69 (15) :2292-2295
[4]   Multioverlap simulations for transitions between reference configurations [J].
Berg, BA ;
Noguchi, H ;
Okamoto, Y .
PHYSICAL REVIEW E, 2003, 68 (03) :11-361261
[5]   MULTICANONICAL ALGORITHMS FOR 1ST ORDER PHASE-TRANSITIONS [J].
BERG, BA ;
NEUHAUS, T .
PHYSICS LETTERS B, 1991, 267 (02) :249-253
[6]   MULTICANONICAL ENSEMBLE - A NEW APPROACH TO SIMULATE 1ST-ORDER PHASE-TRANSITIONS [J].
BERG, BA ;
NEUHAUS, T .
PHYSICAL REVIEW LETTERS, 1992, 68 (01) :9-12
[7]   A COMPARISON OF CONSTANT ENERGY, CONSTANT TEMPERATURE AND CONSTANT PRESSURE ENSEMBLES IN MOLECULAR-DYNAMICS SIMULATIONS OF ATOMIC LIQUIDS [J].
BROWN, D ;
CLARKE, JHR .
MOLECULAR PHYSICS, 1984, 51 (05) :1243-1252
[8]   COMPUTER EXPERIMENT FOR NON-LINEAR THERMODYNAMICS OF COUETTE-FLOW [J].
EVANS, DJ .
JOURNAL OF CHEMICAL PHYSICS, 1983, 78 (06) :3297-3302
[9]   Characteristic temperatures of folding of a small peptide [J].
Hansmann, UHE ;
Masuya, M ;
Okamoto, Y .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1997, 94 (20) :10652-10656
[10]   Molecular dynamics, Langevin and hybrid Monte Carlo simulations in a multicanonical ensemble [J].
Hansmann, UHE ;
Okamoto, Y ;
Eisenmenger, F .
CHEMICAL PHYSICS LETTERS, 1996, 259 (3-4) :321-330