The computer simulation of many molecular processes is complicated by long time scales caused by rare transitions between long-lived states. Here, we propose a new approach to simulate such rare events, which combines transition path sampling with enhanced exploration of configuration space. The method relies on exchange moves between configuration and trajectory space, carried out based on a generalized ensemble. This scheme substantially enhances the efficiency of the transition path sampling simulations, particularly for systems with multiple transition channels, and yields information on thermodynamics, kinetics and reaction coordinates of molecular processes without distorting their dynamics. The method is illustrated using the isomerization of proline in the KPTP tetrapeptide.
翻译:许多分子过程的计算机模拟由于寿命长的状态之间很少的转变造成的长期规模而变得复杂。 这里, 我们提出一种新的模拟这种稀有事件的方法, 将过渡路径取样与加强配置空间的探索结合起来。 这种方法依赖于基于普遍共性进行的配置和轨道空间之间的交换移动。 这个方法大大提高了过渡路径取样模拟的效率, 特别是具有多个过渡通道的系统, 并生成关于热动力学、动能学和分子过程反应坐标的信息, 而不扭曲其动态。 这种方法用KPTP四倍平底线的分解法来说明。