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首页> 外文期刊>The Journal of Chemical Physics >Foundations and latest advances in replica exchange transition interface sampling
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Foundations and latest advances in replica exchange transition interface sampling

机译：副本交换转换界面采样的基础和最新进步

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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.
机译：近20年前，过渡路径采样（TPS）作为自由能量方法的替代方法，用于研究稀有事件，例如成核，蛋白质折叠，化学反应和相转变。 TPS有效地执行了具有相对短的分子动力学轨迹的蒙特卡罗模拟，其优点是不必改变实际潜在的能量表面，也不是潜在的物理动态。尽管TPS方法还引入了计算反应速率的方法，但这种方法是长时间被认为理论上有吸引力，提供了与大多数相关应用的完全相同的结果，但对于大多数相关应用仍然昂贵。随着算法方法的计算机功率和改进的增加，定量路径采样正在越来越多的研究领域寻找应用。特别地，转换界面采样（TIS）和副本交换TIS（RETIS）算法又提高了定量路径采样的效率，同时保持了方法的确切性质。此外，开源软件包正在进行这些方法，其中实现不简单，现在可用于更广泛的用户组。此外，盛开的开发是关于应用程序和算法改进的开发开发。因此，它是及时探索这一领域新发展的广泛全景。这是本文的目的，它侧重于最有效的确切路径采样方法，重新调整，以及最近的应用程序，扩展和变化。通过AIP发布发布。

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