Application of the 2PT model to understanding entropy change in molecular coarse-graining

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.