On the use of transition matrix methods with extended ensembles

被引:31
作者
Escobedo, FA [1 ]
Abreu, CRA [1 ]
机构
[1] Cornell Univ, Sch Chem & Biomol Engn, Ithaca, NY 14853 USA
基金
美国国家科学基金会;
关键词
D O I
10.1063/1.2174010
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
Different extended ensemble schemes for non-Boltzmann sampling (NBS) of a selected reaction coordinate lambda were formulated so that they employ (i) "variable" sampling window schemes (that include the "successive umbrella sampling" method) to comprehensibly explore the lambda domain and (ii) transition matrix methods to iteratively obtain the underlying free-energy eta landscape (or "importance" weights) associated with lambda. The connection between "acceptance ratio" and transition matrix methods was first established to form the basis of the approach for estimating eta(lambda). The validity and performance of the different NBS schemes were then assessed using as lambda coordinate the configurational energy of the Lennard-Jones fluid. For the cases studied, it was found that the convergence rate in the estimation of eta is little affected by the use of data from high-order transitions, while it is noticeably improved by the use of a broader window of sampling in the variable window methods. Finally, it is shown how an "elastic" window of sampling can be used to effectively enact (nonuniform) preferential sampling over the lambda domain, and how to stitch the weights from separate one-dimensional NBS runs to produce a eta surface over a two-dimensional domain. (c) 2006 American Institute of Physics.
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页数:11
相关论文
共 42 条
[1]   A general framework for non-Boltzmann Monte Carlo sampling [J].
Abreu, CRA ;
Escobedo, FA .
JOURNAL OF CHEMICAL PHYSICS, 2006, 124 (05)
[2]  
[Anonymous], J PHYS
[3]   Determination of equilibrium properties of biomolecular systems using multidimensional adaptive umbrella sampling [J].
Bartels, C ;
Schaefer, M ;
Karplus, M .
JOURNAL OF CHEMICAL PHYSICS, 1999, 111 (17) :8048-8067
[4]   EFFICIENT ESTIMATION OF FREE-ENERGY DIFFERENCES FROM MONTE-CARLO DATA [J].
BENNETT, CH .
JOURNAL OF COMPUTATIONAL PHYSICS, 1976, 22 (02) :245-268
[5]   NEW APPROACH TO SPIN-GLASS SIMULATIONS [J].
BERG, BA ;
CELIK, T .
PHYSICAL REVIEW LETTERS, 1992, 69 (15) :2292-2295
[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]   Solid-liquid phase coexistence of the Lennard-Jones system through phase-switch Monte Carlo simulation [J].
Errington, JR .
JOURNAL OF CHEMICAL PHYSICS, 2004, 120 (07) :3130-3141
[8]   Direct calculation of liquid-vapor phase equilibria from transition matrix Monte Carlo simulation [J].
Errington, JR .
JOURNAL OF CHEMICAL PHYSICS, 2003, 118 (22) :9915-9925
[9]   A unified methodological framework for the simulation of nonisothermal ensembles [J].
Escobedo, FA .
JOURNAL OF CHEMICAL PHYSICS, 2005, 123 (04)
[10]   MONTE-CARLO SIMULATION OF THE CHEMICAL-POTENTIAL OF POLYMERS IN AN EXPANDED ENSEMBLE [J].
ESCOBEDO, FA ;
DEPABLO, JJ .
JOURNAL OF CHEMICAL PHYSICS, 1995, 103 (07) :2703-2710