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基于柯克伍德抽样的平衡分子热力学。

Equilibrium molecular thermodynamics from Kirkwood sampling.

作者信息

Somani Sandeep, Okamoto Yuko, Ballard Andrew J, Wales David J

机构信息

†University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, United Kingdom.

‡Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan.

出版信息

J Phys Chem B. 2015 May 21;119(20):6155-69. doi: 10.1021/acs.jpcb.5b01800. Epub 2015 May 12.

DOI:10.1021/acs.jpcb.5b01800
PMID:25915525
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4500650/
Abstract

We present two methods for barrierless equilibrium sampling of molecular systems based on the recently proposed Kirkwood method (J. Chem. Phys. 2009, 130, 134102). Kirkwood sampling employs low-order correlations among internal coordinates of a molecule for random (or non-Markovian) sampling of the high dimensional conformational space. This is a geometrical sampling method independent of the potential energy surface. The first method is a variant of biased Monte Carlo, where Kirkwood sampling is used for generating trial Monte Carlo moves. Using this method, equilibrium distributions corresponding to different temperatures and potential energy functions can be generated from a given set of low-order correlations. Since Kirkwood samples are generated independently, this method is ideally suited for massively parallel distributed computing. The second approach is a variant of reservoir replica exchange, where Kirkwood sampling is used to construct a reservoir of conformations, which exchanges conformations with the replicas performing equilibrium sampling corresponding to different thermodynamic states. Coupling with the Kirkwood reservoir enhances sampling by facilitating global jumps in the conformational space. The efficiency of both methods depends on the overlap of the Kirkwood distribution with the target equilibrium distribution. We present proof-of-concept results for a model nine-atom linear molecule and alanine dipeptide.

摘要

我们基于最近提出的柯克伍德方法（《化学物理杂志》2009年，第130卷，第134102页），介绍了两种用于分子系统无障碍平衡采样的方法。柯克伍德采样利用分子内部坐标之间的低阶相关性，对高维构象空间进行随机（或非马尔可夫）采样。这是一种独立于势能面的几何采样方法。第一种方法是有偏蒙特卡罗的变体，其中柯克伍德采样用于生成试验性蒙特卡罗移动。使用这种方法，可以从给定的一组低阶相关性生成对应于不同温度和势能函数的平衡分布。由于柯克伍德样本是独立生成的，这种方法非常适合大规模并行分布式计算。第二种方法是储库复制交换的变体，其中柯克伍德采样用于构建一个构象储库，该储库与对应于不同热力学状态进行平衡采样的复制品交换构象。与柯克伍德储库的耦合通过促进构象空间中的全局跳跃来增强采样。两种方法的效率都取决于柯克伍德分布与目标平衡分布的重叠。我们给出了一个九原子线性模型分子和丙氨酸二肽的概念验证结果。

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