Automated sampling assessment for molecular simulations using the effective sample size.
Automated sampling assessment for molecular simulations using the effective sample size.
复制标题
使用有效样本量对分子模拟进行自动采样评估。
DOI：
10.1021/ct1002384
复制
发表时间：
2010
影响因子：
5.5
通讯作者：
Zuckerman,DanielM
中科院分区：
文献类型：
--
作者：
Zhang,Xin;Bhatt,Divesh;Zuckerman,DanielM
为了量化分子模拟中使用的算法和力场的发展进展，需要一种用于评估采样质量的通用方法。统计力学原理表明，物理状态的总体以基本的方式表征平衡采样。因此，我们开发了一种方法来分析状态人口的方差，量化的有效样本量（ESS）的抽样程度。ESS估计模拟系综中包含的统计独立配置的数量。该方法适用于传统的动力学模拟以及更现代的（例如，multicanonical）方法。我们的程序在各种系统中进行测试，从玩具模型到原子蛋白质模拟。我们还介绍了一个简单的自动化程序，以获得近似的物理状态，从动态轨迹：这使得样本量估计系统的物理状态是不知道的。
To quantify the progress in the development of algorithms and force fields used in molecular simulations, a general method for the assessment of the sampling quality is needed. Statistical mechanics principles suggest the populations of physical states characterize equilibrium sampling in a fundamental way. We therefore develop an approach for analyzing the variances in state populations, which quantifies the degree of sampling in terms of the effective sample size (ESS). The ESS estimates the number of statistically independent configurations contained in a simulated ensemble. The method is applicable to both traditional dynamics simulations as well as more modern (e.g., multicanonical) approaches. Our procedure is tested in a variety of systems from toy models to atomistic protein simulations. We also introduce a simple automated procedure to obtain approximate physical states from dynamic trajectories: this allows sample-size estimation in systems for which physical states are not known in advance.