Fep1d: a script for the analysis of reaction coordinates.
Fep1d: a script for the analysis of reaction coordinates.
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Fep1d：用于分析反应坐标的脚本。
DOI：
10.1002/jcc.23868
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发表时间：
2015
影响因子：
3
通讯作者：
Banushkina PV
中科院分区：
文献类型：
--
作者：
Banushkina PV
具有多个自由度的复杂系统的动力学可以通过将其投影到一个或几个坐标(集合变量)来进行分析。这种动力学当时通常被描述为在与坐标相关的自由能地貌上的扩散。Fep1d是用于分析这种一维坐标的脚本。该脚本允许用户构建常规的和基于切割的自由能分布，评估反应坐标的最佳性，检查投影在坐标上的动力学是否扩散，将反应坐标变换(重新定标)为更方便的坐标，并计算平均第一次通过时间、过渡路径时间、坐标相关的扩散系数等量。在这里，我们描述了实现的功能以及基本的理论框架。©2015 Wiley期刊，Inc.
The dynamics of complex systems with many degrees of freedom can be analyzed by projecting it onto one or few coordinates (collective variables). The dynamics is often described then as diffusion on a free energy landscape associated with the coordinates. Fep1d is a script for the analysis of such one‐dimensional coordinates. The script allows one to construct conventional and cut‐based free energy profiles, to assess the optimality of a reaction coordinate, to inspect whether the dynamics projected on the coordinate is diffusive, to transform (rescale) the reaction coordinate to more convenient ones, and to compute such quantities as the mean first passage time, the transition path times, the coordinate dependent diffusion coefficient, and so forth. Here, we describe the implemented functionality together with the underlying theoretical framework. © 2015 Wiley Periodicals, Inc.