Advances in milestoning. I. Enhanced sampling via wind-assisted reweighted milestoning (WARM)
Advances in milestoning. I. Enhanced sampling via wind-assisted reweighted milestoning (WARM)
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DOI：
10.1063/1.5029954
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发表时间：
2018-08-28
影响因子：
4.4
通讯作者：
Andricioaei, Ioan
中科院分区：
文献类型：
--
作者：
Grazioli, Gianmarc;Andricioaei, Ioan
Elber 及其同事的里程碑算法创建了一个框架，用于计算过程的时间尺度，这些过程太长且太复杂，无法使用简单的强力模拟进行研究。里程碑算法中涉及的基本对象是相邻构象里程碑 A 和 B 之间的首次通过时间分布 K-AB(tau)。本文提出的方法旨在通过采用人工施加的力（类似于将轨迹从初始状态吹到最终状态的风）来进一步增强里程碑（或其他基于界面的采样方法），并随后对轨迹应用校正权重以在分数中产生真实的首次通过时间分布 K-AB(tau)独立计算所需的计算时间。重新加权方法植根于随机路径积分的形式主义。介绍了该技术的理论基础和数值例子。由 AIP 出版社出版。
The milestoning algorithm of Elber and co-workers creates a framework for computing the time scale of processes that are too long and too complex to be studied using simply brute force simulations. The fundamental objects involved in the milestoning algorithm are the first passage time distributions K-AB(tau) between adjacent conformational milestones A and B. The method proposed herein aims to further enhance milestoning (or other interface based sampling methods) by employing an artificially applied force, akin to a wind that blows the trajectories from their initial to their final states, and by subsequently applying corrective weights to the trajectories to yield the true first passage time distributions K-AB(tau) in a fraction of the computation time required for unassisted calculations. The re-weighting method is rooted in the formalism of stochastic path integrals. The theoretical basis for the technique and numerical examples are presented. Published by AIP Publishing.