Simple Quantitative Tests to Validate Sampling from Thermodynamic Ensembles.
Simple Quantitative Tests to Validate Sampling from Thermodynamic Ensembles.
复制标题
DOI：
10.1021/ct300688p
复制
发表时间：
2012-08
影响因子：
5.5
通讯作者：
Michael R. Shirts
中科院分区：
文献类型：
--
作者：
Michael R. Shirts
通常很难定量地确定新的分子模拟算法或软件是否正确地实现了对所需热力学系综的采样。我们提供了一些简单的统计分析程序，以允许灵敏地确定所需的热力学系综是否被适当采样。这些程序使用成对模拟来抵消依赖于系统的态密度，并直接测试与系综相关联的玻尔兹曼分布(通常为正则、等压-等温或大正则)的满足程度。我们演示了这些测试在一系列情况下对模型系统和分子动力学模拟的效用，并描述了为最终用户设计的测试的实现。
It is often difficult to quantitatively determine if a new molecular simulation algorithm or software properly implements sampling of the desired thermodynamic ensemble. We present some simple statistical analysis procedures to allow sensitive determination of whether the desired thermodynamic ensemble is properly sampled. These procedures use paired simulations to cancel out system dependent densities of state and directly test the extent to which the Boltzmann distribution associated with the ensemble (usually canonical, isobaric-isothermal, or grand canonical) is satisfied. We demonstrate the utility of these tests for model systems and for molecular dynamics simulations in a range of situations and describe an implementation of the tests designed for end users.