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:很多分子过程的计算机模拟都存在由于长时间尺度而产生的长寿命态间的稀有转变。在这里,我们提出了一种新的方法来模拟这样的稀有事件,它结合了过渡路径抽样技术和构型空间的增强探索。该方法依赖于构型空间和轨迹空间之间的交换移动,基于一个广义集合进行。这种方案极大地增强了过渡路径抽样模拟的效率,特别是对于具有多个转变通道的系统,并且在不扭曲它们的动态学的情况下提供了有关分子过程的热力学、动力学和反应坐标的信息。该方法以KPTP四肽中脯氨酸异构化为例进行了演示。