The algorithmic development in the field of path sampling has made tremendous progress in recent years. Although the original transition path sampling method was mostly used as a qualitative tool to sample reaction paths, the more recent family of interface‐based path sampling methods has paved the way for more quantitative rate calculation studies. Of the exact methods, the replica exchange transition interface sampling (RETIS) method is the most efficient, but rather difficult to implement. This has been the main motivation to develop the open‐source Python‐based computer library PyRETIS that was released in 2017. PyRETIS is designed to be easily interfaced with any molecular dynamics (MD) package using either classical or ab initio MD. In this study, we report on the principles and the software enhancements that are now included in PyRETIS 2, as well as the recent developments on the user interface, improvements of the efficiency via the implementation of new shooting moves, easier initialization procedures, analysis methods, and supported interfaced software. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.

中文翻译：

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PyRETIS 2：罕见事件的可能性驱动

近年来，路径采样领域的算法发展取得了巨大的进步。尽管最初的过渡路径采样方法主要用作对反应路径进行采样的定性工具，但最近的基于界面的路径采样方法系列为更多的定量速率计算研究铺平了道路。在确切的方法中，副本交换转换接口采样（RETIS）方法是最有效的，但实现起来却相当困难。这是开发 2017 年发布的基于 Python 的开源计算机库 PyRETIS 的主要动机。 PyRETIS 旨在使用经典或 ab initio MD 与任何分子动力学 (MD) 包轻松连接。在这项研究中，我们报告了现在包含在 PyRETIS 2 中的原则和软件增强功能，以及用户界面的最新发展，通过实施新的射击动作、更简单的初始化程序、分析方法和支持的接口软件来提高效率。© 2019 作者。Wiley Periodicals, Inc. 出版的《计算化学杂志》。