A one-way shooting algorithm for transition path sampling of asymmetric barriers

被引：30

作者：

Brotzakis, Z. Faidon ^{[1
]}

Bolhuis, Peter G. ^{[1
]}

机构：

[1] Univ Amsterdam, Vant Hoff Inst Mol Sci, POB 94157, NL-1090 GD Amsterdam, Netherlands

来源：

JOURNAL OF CHEMICAL PHYSICS | 2016年 / 145卷 / 16期

关键词：

MOLECULAR-DYNAMICS METHOD; RATE CONSTANTS; SIMULATION; SYSTEMS; FORCE; WATER;

D O I：

10.1063/1.4965882

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 present a novel transition path sampling shooting algorithm for the efficient sampling of complex (biomolecular) activated processes with asymmetric free energy barriers. The method employs a fictitious potential that biases the shooting point toward the transition state. The method is similar in spirit to the aimless shooting technique by Peters and Trout [J. Chem. Phys. 125, 054108 (2006)], but is targeted for use with the one-way shooting approach, which has been shown to be more effective than two-way shooting algorithms in systems dominated by diffusive dynamics. We illustrate the method on a 2D Langevin toy model, the association of two peptides and the initial step in dissociation of a beta-lactoglobulin dimer. In all cases we show a significant increase in efficiency. Published by AIP Publishing.

引用

页数：12

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