Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom.
Van't Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands.
J Chem Phys. 2019 Nov 7;151(17):174111. doi: 10.1063/1.5119252.
Transition path sampling is a powerful technique for investigating rare transitions, especially when the mechanism is unknown and one does not have access to the reaction coordinate. Straightforward application of transition path sampling does not directly provide the free energy landscape nor the kinetics. This drawback has motivated the development of path sampling extensions able to simultaneously access both kinetics and thermodynamics, such as transition interface sampling, and the reweighted path ensemble. However, performing transition interface sampling is more involved than standard two-state transition path sampling and still requires (some) insight into the reaction to define interfaces. While packages that can efficiently compute path ensembles for transition interface sampling are now available, it would be useful to directly compute the free energy from a single standard transition path sampling simulation. To achieve this, we present here an approximate method, denoted virtual interface exchange transition path sampling, that makes use of the rejected pathways in a form of waste recycling. The method yields an approximate reweighted path ensemble that allows an immediate view of the free energy landscape from a standard single transition path sampling simulation, as well as enables a committor analysis.
迁移路径采样是一种强大的技术，可用于研究罕见的跃迁，尤其是在机制未知且无法获得反应坐标的情况下。简单地应用迁移路径采样并不能直接提供自由能景观或动力学。这一缺点促使人们开发了能够同时访问动力学和热力学的路径采样扩展方法，例如迁移界面采样和重新加权路径集合。然而，执行迁移界面采样比标准的两态迁移路径采样更为复杂，并且仍然需要（一些）对反应的了解来定义界面。虽然现在已经有了可以高效计算迁移界面采样路径集合的软件包，但直接从单个标准迁移路径采样模拟中计算自由能将是非常有用的。为了实现这一点，我们在这里提出了一种近似方法，称为虚拟界面交换迁移路径采样，它以废物回收的形式利用被拒绝的路径。该方法产生了一个近似的重新加权路径集合，允许从标准的单个迁移路径采样模拟中立即观察自由能景观，并能够进行连接分析。
