Bolhuis Peter G
van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018WV Amsterdam, The Netherlands.
J Chem Phys. 2008 Sep 21;129(11):114108. doi: 10.1063/1.2976011.
Transition path sampling (TPS) was developed for studying activated processes in complex systems with unknown reaction coordinate. Transition interface sampling (TIS) allows efficient evaluation of the rate constants. However, when the transition can occur via more than one reaction channel separated by a high barrier, TPS and TIS are ineffective in sampling both channels. The combination of replica exchange with TIS can overcome this problem. This work shows how, by including both the backward and forward reactions, the corresponding rate constants, as well as the free energy barrier can be computed in a single simulation. The method is illustrated on a two dimensional potential using the Langevin dynamics. In addition, a simpler algorithm based on only forward shooting from the interfaces is shown to give equally accurate results, and forms a bridge between the transition interface and the forward flux sampling methods. The diffusive behavior of the replicas can be used to assess the quality of the choice of the order parameter used for the interfaces.
过渡路径采样(TPS)是为研究具有未知反应坐标的复杂系统中的活化过程而开发的。过渡界面采样(TIS)能够有效评估速率常数。然而,当过渡可以通过由高势垒分隔的多个反应通道发生时,TPS和TIS在对两个通道进行采样时效率低下。副本交换与TIS相结合可以克服这个问题。这项工作展示了如何通过同时包含正向和反向反应,在单次模拟中计算相应的速率常数以及自由能垒。该方法在二维势场上使用朗之万动力学进行了说明。此外,还展示了一种仅基于从界面进行正向射击的更简单算法,该算法能给出同样准确的结果,并在过渡界面和正向通量采样方法之间架起了一座桥梁。副本的扩散行为可用于评估用于界面的序参量选择的质量。