Phase space and collective variable based simulation methods for studies of rare events
Phase space and collective variable based simulation methods for studies of rare events
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DOI：
10.1080/08927022.2019.1634268
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发表时间：
2019-06-29
影响因子：
2.1
通讯作者：
Vashisth, Harish
中科院分区：
文献类型：
--
作者：
Paul, Sanjib;Nair, Nisanth N.;Vashisth, Harish
在这项工作中，我们回顾了研究罕见事件的分子模拟方法。特别强调的是最近的进展和生物应用的方法，利用无偏采样在全相空间中发现反应轨迹和他们的合奏，以及利用有偏采样沿着集体变量，以有效地采样自由能景观的方法。在相空间方法中，我们讨论了过渡路径采样及其变体，并通过过渡路径理论，反应岛和拉格朗日描述符突出反应轨迹分析中出现的主题。在集体变量方法中，我们讨论了允许在高维CV空间中进行有效采样的技术，无论是通过基于复制的方法，还是通过为每个CV调用独立的采样协议。具体而言，我们强调了两个变体的元自相关方法，偏置交换和平行偏置元自相关，和一种混合方法，称为温度加速切片采样，已被设计为克服相关方法的局限性。
In this work, we review molecular simulation methods for studies of rare events. Specifically highlighted are recent advances and biological applications of methods that utilise unbiased sampling in full phase space to discover reactive trajectories and their ensembles as well as methods that utilise biased sampling along collective variables to efficiently sample free energy landscapes. Among phase space methods, we discuss transition path sampling and its variants and highlight emerging themes in analyses of reactive trajectories via transition path theory, reactive islands, and Lagrangian descriptors. Among collective variable methods, we discuss techniques that allow efficient sampling in a high-dimensional CV space, either via replica-based approaches or by invoking an independent sampling protocol for each CV. Specifically, we highlight two variants of the metadynamics method, bias-exchange and parallel-bias metadynamics, and a hybrid method termed temperature-accelerated sliced sampling, that have been designed to overcome limitations of related approaches.