ABSTRACT

The effects of coarse-graining on the thermodynamic properties of molecular liquids are studied by computing the standard molar entropies of chloroform, 1,4-dioxane and neopentane using the two-phase thermodynamic (2PT) model. From the trajectory of molecular dynamics simulations, the entropy associated with changing the level of resolution is measured. The entropic contribution coming from the choice of the mapping and from the coarse-grained force field is decoupled. The entropy of the eliminated degrees of freedom is estimated from the rerun of the mapped trajectory, while the additional entropy variation, tied to the coarse-grained force field itself, is quantified by subtraction. In this work the 2PT model is used as a diagnostic tool to analyze how different mappings schemes affect the dynamic modes of the molecules and to quantify the change in entropy. Good agreement between the target density of states of the mapped trajectory and the coarse-grained distribution of normal modes is found. The entropy change upon coarse-graining is discussed in terms of vibrational, rotational, and translational contributions.

摘要

通过使用两相热力学（2PT）模型计算氯仿，1,4-二恶烷和新戊烷的标准摩尔熵，研究了粗粒度对分子液体热力学性质的影响。从分子动力学模拟的轨迹，可以测量与改变分辨率水平相关的熵。来自映射的选择和来自粗粒度力场的熵贡献被解耦。消除的自由度的熵是从映射轨迹的重新估计而来的，而与粗粒度力场本身相关的附加熵的变化是通过减法来量化的。在这项工作中，将2PT模型用作诊断工具，以分析不同的映射方案如何影响分子的动态模式并量化熵的变化。在映射轨迹的状态目标密度与法线模式的粗粒度分布之间找到了很好的一致性。根据振动，旋转和平移的影响讨论了粗粒度时的熵变化。