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复制交换过渡界面采样和前向通量采样实用指南。

Practical guide to replica exchange transition interface sampling and forward flux sampling.

机构信息

Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, USA.

Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridgeshire CB2 1EW, United Kingdom.

出版信息

J Chem Phys. 2022 May 28;156(20):200901. doi: 10.1063/5.0080053.

Abstract

Path sampling approaches have become invaluable tools to explore the mechanisms and dynamics of the so-called rare events that are characterized by transitions between metastable states separated by sizable free energy barriers. Their practical application, in particular to ever more complex molecular systems, is, however, not entirely trivial. Focusing on replica exchange transition interface sampling (RETIS) and forward flux sampling (FFS), we discuss a range of analysis tools that can be used to assess the quality and convergence of such simulations, which is crucial to obtain reliable results. The basic ideas of a step-wise evaluation are exemplified for the study of nucleation in several systems with different complexities, providing a general guide for the critical assessment of RETIS and FFS simulations.

摘要

路径采样方法已成为探索所谓稀有事件机制和动力学的宝贵工具,这些稀有事件的特征是通过由相当大的自由能势垒隔开的亚稳态之间的转变。然而,将其实际应用于越来越复杂的分子系统并不完全简单。本文聚焦于复制交换跃迁界面采样(RETIS)和正向通量采样(FFS),讨论了一系列可用于评估此类模拟的质量和收敛性的分析工具,这对于获得可靠的结果至关重要。逐步评估的基本思想通过对几个具有不同复杂性的体系中成核的研究进行举例说明,为 RETIS 和 FFS 模拟的关键评估提供了一般指南。

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