Improved Wang-Landau sampling through the use of smoothed potential-energy surfaces

被引:6
作者
Nguyen, PH
Mittag, E
Torda, AE
Stock, G
机构
[1] Goethe Univ Frankfurt, Inst Phys & Theoret Chem, D-60439 Frankfurt, Germany
[2] Univ Hamburg, Ctr Bioinformat, D-20146 Hamburg, Germany
[3] Goethe Univ Frankfurt, Inst Phys & Theoret Chem, D-60439 Frankfurt, Germany
关键词
D O I
10.1063/1.2191060
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
A method is presented to improve the speed of convergence of Wang-Landau simulations as used to calculate the density of states of continuous systems. The density of states is first crudely estimated with calculations employing a smoothed potential-energy surface. This estimate is then used as a seed for subsequent Wang-Landau simulations using the original potential. The performance of the method is demonstrated by employing several simple models, including an analytically solvable harmonic system as well as a Go $$($) over bar model of a protein. For all systems considered, the seeded simulations were found to converge significantly faster and with higher accuracy than the standard Wang-Landau simulations. (c) 2006 American Institute of Physics.
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页数:6
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共 41 条
[1]   On monte carlo and molecular dynamics methods inspired by Tsallis statistics: Methodology, optimization, and application to atomic clusters [J].
Andricioaei, I ;
Straub, JE .
JOURNAL OF CHEMICAL PHYSICS, 1997, 107 (21) :9117-9124
[2]   Generalized simulated annealing algorithms using Tsallis statistics: Application to conformational optimization of a tetrapeptide [J].
Andricioaei, I ;
Straub, JE .
PHYSICAL REVIEW E, 1996, 53 (04) :R3055-R3058
[3]  
[Anonymous], 1987, Introduction to Modern Statistical Mechanics
[4]   Algorithmic aspects of multicanonical simulations [J].
Berg, BA .
NUCLEAR PHYSICS B-PROCEEDINGS SUPPLEMENTS, 1998, 63 :982-984
[5]   Generalized ensemble simulations for complex systems [J].
Berg, BA .
COMPUTER PHYSICS COMMUNICATIONS, 2002, 147 (1-2) :52-57
[6]   MULTICANONICAL ALGORITHMS FOR 1ST ORDER PHASE-TRANSITIONS [J].
BERG, BA ;
NEUHAUS, T .
PHYSICS LETTERS B, 1991, 267 (02) :249-253
[7]   MULTICANONICAL ENSEMBLE - A NEW APPROACH TO SIMULATE 1ST-ORDER PHASE-TRANSITIONS [J].
BERG, BA ;
NEUHAUS, T .
PHYSICAL REVIEW LETTERS, 1992, 68 (01) :9-12
[8]  
Berg BA, 2005, LECT NOTES SER INST, V7, P1
[9]   The Protein Data Bank [J].
Berman, HM ;
Westbrook, J ;
Feng, Z ;
Gilliland, G ;
Bhat, TN ;
Weissig, H ;
Shindyalov, IN ;
Bourne, PE .
NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :235-242
[10]   Novel methods of sampling phase space in the simulation of biological systems [J].
Berne, BJ ;
Straub, JE .
CURRENT OPINION IN STRUCTURAL BIOLOGY, 1997, 7 (02) :181-189