Foundations and latest advances in replica exchange transition interface sampling
Foundations and latest advances in replica exchange transition interface sampling
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DOI：
10.1063/1.4989844
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发表时间：
2017-10-21
影响因子：
4.4
通讯作者：
van Erp, Titus S.
中科院分区：
文献类型：
--
作者：
Cabriolu, Raffaela;Refsnes, Kristin M. Skjelbred;van Erp, Titus S.
近20年前，过渡路径采样（TPS）作为基于自由能的方法的替代方法出现，用于研究罕见事件，如成核，蛋白质折叠，化学反应和相变。TPS有效地执行Monte Carlo模拟与相对较短的分子动力学轨迹，具有不必改变实际的势能面，也没有底层的物理动力学的优点。虽然TPS方法也引入了一种计算反应速率的方法，但这种方法在很长一段时间内被认为是理论上有吸引力的，提供了与长时间分子动力学模拟完全相同的结果，但对于大多数相关应用来说仍然昂贵。随着计算机处理能力的提高和算法方法的改进，定量路径抽样在越来越多的研究领域得到了应用。特别是，过渡接口采样（TIS）和副本交换TIS（RETIS）算法，反过来，提高了效率的定量路径采样显着，同时保持了确切的性质的方法。此外，开放源码软件包正在使这些实施起来并不简单的方法现在可供更广泛的用户使用。此外，在应用程序和算法改进方面都有了蓬勃发展。因此，探讨这一领域新发展的广泛全景是及时的。这是本文的目的，重点介绍最有效的精确路径采样方法，RETIS，以及它最近的应用，扩展和变化。出版社：AIP Publishing
Nearly 20 years ago, transition path sampling (TPS) emerged as an alternative method to free energy based approaches for the study of rare events such as nucleation, protein folding, chemical reactions, and phase transitions. TPS effectively performs Monte Carlo simulations with relatively short molecular dynamics trajectories, with the advantage of not having to alter the actual potential energy surface nor the underlying physical dynamics. Although the TPS approach also introduced a methodology to compute reaction rates, this approach was for a long time considered theoretically attractive, providing the exact same results as extensively long molecular dynamics simulations, but still expensive for most relevant applications. With the increase of computer power and improvements in the algorithmic methodology, quantitative path sampling is finding applications in more and more areas of research. In particular, the transition interface sampling (TIS) and the replica exchange TIS (RETIS) algorithms have, in turn, improved the efficiency of quantitative path sampling significantly, while maintaining the exact nature of the approach. Also, open-source software packages are making these methods, for which implementation is not straightforward, now available for a wider group of users. In addition, a blooming development takes place regarding both applications and algorithmic refinements. Therefore, it is timely to explore the wide panorama of the new developments in this field. This is the aim of this article, which focuses on the most efficient exact path sampling approach, RETIS, as well as its recent applications, extensions, and variations. Published by AIP Publishing.