基于时间可逆性的动力学加速算法tRPS
时间：2023-12-29
Zhirong Liu*. Accelerating kinetics with time-reversal path sampling. Molecules 28 (24), 8147/1-12 (2023).
导读: 热力学和动力学是物理化学的两个重要内容。一般而言，热力学性质的模拟比动力学容易一些。基于玻尔兹曼分布以及其它的平衡统计规律，已经开发了各种有效的增强采样方法来加快热力学的分子模拟速度。与此相比，动力学和非平衡统计的加速模拟方法相对较少，效果也没那么理想。针对这个问题，我们基于微观动力学过程的时间可逆对称性，提出了一种称为时间可逆路径采样（time-reversal path sampling，简称为tRPS）的方法，以实现分子模拟的动力学加速。
Abstract: In comparison to numerous enhanced sampling methods for equilibrium thermodynamics, accelerating simulations for kinetics and nonequilibrium statistics are relatively rare and less effective. Here we derive a time-reversal path sampling (tRPS) method based on the time reversibility to accelerate simulations for determining the transition rates between free-energy basins. It converts the difficult up-hill path sampling into an easy down-hill problem. The method is easy to implement, i.e., forward and backward shooting simulations with opposite initial velocities are conducted from random initial conformations within a transition-state region until they reach the basin minima, which are then assembled to give the distribution of transition paths efficiently. The effects of tRPS are demonstrated by comparison with direct simulations on protein folding and unfolding, where tRPS is shown to give results consistent with direct simulations and increase the efficiency by up to five orders of magnitude. The approach is generally applicable to stochastic processes with microscopic reversibility, no matter whether the variables are continuous or discrete.
