Li Wenjin, Ma Ao
Department of Bioengineering, The University of Illinois at Chicago, 851 South Morgan Street, Chicago, IL 60607, USA.
Mol Simul. 2014;40(10-11):784-793. doi: 10.1080/08927022.2014.907898.
In the study of rare events in complex systems with many degrees of freedom, a key element is to identify the reaction coordinates of a given process. Over recent years, a number of methods and protocols have been developed to extract the reaction coordinates based on limited information from molecular dynamics simulations. In this review, we provide a brief survey over a number of major methods developed in the past decade, some of which are discussed in greater detail, to provide an overview of the problems that are partially solved and challenges that still remain. A particular emphasis has been placed on methods for identifying reaction coordinates that are related to the committor.
在具有多个自由度的复杂系统中对稀有事件的研究中，一个关键要素是确定给定过程的反应坐标。近年来，已经开发了许多方法和协议，用于根据分子动力学模拟中的有限信息来提取反应坐标。在本综述中，我们简要概述了过去十年中开发的一些主要方法，其中一些方法将进行更详细的讨论，以概述部分已解决的问题和仍然存在的挑战。特别强调了与反应几率相关的反应坐标识别方法。
