Enhanced Sampling of Nonequilibrium Steady States

被引:74
作者
Dickson, Alex [1 ]
Dinner, Aaron R.
机构
[1] Univ Chicago, James Franck Inst, Dept Chem, Chicago, IL 60637 USA
来源
ANNUAL REVIEW OF PHYSICAL CHEMISTRY, VOL 61 | 2010年 / 61卷
关键词
nonequilibrium umbrella sampling; forward flux sampling; transition rates; path sampling; string method; STOCHASTIC SIMULATION; DYNAMICS SIMULATIONS; SINGLE-MOLECULE; MODELS; TRANSITIONS; SUSPENSIONS; ROBUSTNESS; ENSEMBLE; KINETICS;
D O I
10.1146/annurev.physchem.012809.103433
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 review recent progress in methods for accelerating the convergence of simulations of nonequilibrium systems, specifically nonequilibrium umbrella sampling (NEUS) and forward flux sampling (FFS). These methods account for statistics of dynamical paths between interfaces to enforce sampling of low probability regions of phase space for computing steady-state averages, including transition rates, for systems driven arbitrarily far from equilibrium. Recent advances in NEUS allow for efficient sampling of complex systems by focusing sampling in the vicinity of a one-dimensional manifold (string) that connects regions of interest in phase space; this procedure can be extended to the case of two strings that describe the forward and backward transition ensembles separately, which is useful, as they do not, in general, coincide. We recast FFS in the framework of NEUS to facilitate comparison of the two methods. We conclude by discussing selected applications of interest.
引用
收藏
页码:441 / 459
页数:19
相关论文
共 95 条
[21]   Computational prediction of ion permeation characteristics in the glycine receptor modified by photo-sensitive compounds [J].
Cheng, Mary Hongying ;
Coalson, Rob D. ;
Cascio, Michael ;
Kurnikova, Maria .
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 2008, 22 (08) :563-570
[22]   Homology modeling and molecular dynamics simulations of the α1 glycine receptor reveals different states of the channel [J].
Cheng, Mary Hongying ;
Cascio, Michael ;
Coalson, Rob D. .
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2007, 68 (02) :581-593
[23]   Efficient transition path sampling for nonequilibrium stochastic dynamics [J].
Crooks, GE ;
Chandler, D .
PHYSICAL REVIEW E, 2001, 64 (02) :4-261094
[24]   How to simulate the quasistationary state [J].
de Oliveira, MM ;
Dickman, R .
PHYSICAL REVIEW E, 2005, 71 (01)
[25]   Cyclic motion of a grafted polymer under shear flow [J].
Delgado-Buscalioni, R .
PHYSICAL REVIEW LETTERS, 2006, 96 (08)
[26]   Transition path sampling and the calculation of rate constants [J].
Dellago, C ;
Bolhuis, PG ;
Csajka, FS ;
Chandler, D .
JOURNAL OF CHEMICAL PHYSICS, 1998, 108 (05) :1964-1977
[27]   Transition Path Sampling and Other Advanced Simulation Techniques for Rare Events [J].
Dellago, Christoph ;
Bolhuis, Peter G. .
ADVANCED COMPUTER SIMULATION APPROACHES FOR SOFT MATTER SCIENCES III, 2009, 221 :167-233
[28]   Separating forward and backward pathways in nonequilibrium umbrella sampling [J].
Dickson, Alex ;
Warmflash, Aryeh ;
Dinner, Aaron R. .
JOURNAL OF CHEMICAL PHYSICS, 2009, 131 (15)
[29]   Nonequilibrium umbrella sampling in spaces of many order parameters [J].
Dickson, Alex ;
Warmflash, Aryeh ;
Dinner, Aaron R. .
JOURNAL OF CHEMICAL PHYSICS, 2009, 130 (07)
[30]  
Evans D. J., 2008, STAT MECH NONEQUILIB