A general and efficient Monte Carlo method for sampling intramolecular degrees of freedom of branched and cyclic molecules.
A general and efficient Monte Carlo method for sampling intramolecular degrees of freedom of branched and cyclic molecules.
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一种通用且有效的蒙特卡罗方法，用于对支链和环状分子的分子内自由度进行采样。
DOI：
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发表时间：
2011
影响因子：
4.4
通讯作者：
E. Maginn
中科院分区：
文献类型：
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作者：
J. Shah;E. Maginn
描述了一种简单易行的Monte Carlo算法，该算法能够对含有分支点和含有内环和环外原子的环的分子进行构型偏置采样。该方法克服了与顺序配置偏差采样方法相关的众所周知的问题。产生具有依赖于刚性分子内自由度的已知概率分布的片段的“库”或“库”。偏置移动利用与剩余自由度相关的能量将碎片组装成完整的分子。用于生成片段的方法在丙烷、异丁烷、新戊烷、环己烷和甲基环己烷的模型上进行了验证。它示出了如何在吉布斯系综中实施采样方法，并进行验证研究，其中丙烷，异丁烷，和2，2-二甲基己烷的液体共存曲线进行计算，并显示同意与接受的值。该方法是通用的，可以用来采样任意复杂的分子在开放和封闭的统计力学系综的构象空间。
A simple and easily implemented Monte Carlo algorithm is described which enables configurational-bias sampling of molecules containing branch points and rings with endocyclic and exocyclic atoms. The method overcomes well-known problems associated with sequential configurational-bias sampling methods. A "reservoir" or "library" of fragments are generated with known probability distributions dependent on stiff intramolecular degrees of freedom. Configurational-bias moves assemble the fragments into whole molecules using the energy associated with the remaining degrees of freedom. The methods for generating the fragments are validated on models of propane, isobutane, neopentane, cyclohexane, and methylcyclohexane. It is shown how the sampling method is implemented in the Gibbs ensemble, and validation studies are performed in which the liquid coexistence curves of propane, isobutane, and 2,2-dimethylhexane are computed and shown to agree with accepted values. The method is general and can be used to sample conformational space for molecules of arbitrary complexity in both open and closed statistical mechanical ensembles.