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高效采样原子构型空间。

Efficient sampling of atomic configurational spaces.

机构信息

University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom.

出版信息

J Phys Chem B. 2010 Aug 19;114(32):10502-12. doi: 10.1021/jp1012973.

Abstract

We describe a method to explore the configurational phase space of chemical systems. It is based on the nested sampling algorithm recently proposed by Skilling (AIP Conf. Proc. 2004, 395; J. Bayesian Anal. 2006, 1, 833) and allows us to explore the entire potential energy surface (PES) efficiently in an unbiased way. The algorithm has two parameters which directly control the trade-off between the resolution with which the space is explored and the computational cost. We demonstrate the use of nested sampling on Lennard-Jones (LJ) clusters. Nested sampling provides a straightforward approximation for the partition function; thus, evaluating expectation values of arbitrary smooth operators at arbitrary temperatures becomes a simple postprocessing step. Access to absolute free energies allows us to determine the temperature-density phase diagram for LJ cluster stability. Even for relatively small clusters, the efficiency gain over parallel tempering in calculating the heat capacity is an order of magnitude or more. Furthermore, by analyzing the topology of the resulting samples, we are able to visualize the PES in a new and illuminating way. We identify a discretely valued order parameter with basins and suprabasins of the PES, allowing a straightforward and unambiguous definition of macroscopic states of an atomistic system and the evaluation of the associated free energies.

摘要

我们描述了一种探索化学系统构象相空间的方法。它基于最近由 Skilling 提出的嵌套抽样算法(AIP Conf.Proc. 2004, 395; J. Bayesian Anal. 2006, 1, 833),能够以无偏的方式有效地探索整个势能面(PES)。该算法有两个参数,它们直接控制空间探测的分辨率和计算成本之间的权衡。我们在 Lennard-Jones(LJ)团簇上演示了嵌套抽样的使用。嵌套抽样为配分函数提供了直接的近似,因此,在任意温度下评估任意光滑算子的期望值成为一个简单的后处理步骤。获得绝对自由能使我们能够确定 LJ 团簇稳定性的温度-密度相图。即使对于相对较小的团簇,在计算热容时,与平行温度化相比,效率增益也达到了一个数量级或更多。此外,通过分析得到的样本的拓扑结构,我们能够以一种新的、有启发性的方式可视化 PES。我们确定了一个具有 PES 的盆地和超盆地的离散值序参量,允许对原子系统的宏观状态进行直接而明确的定义,并评估相关的自由能。

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