Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids

Abstract

The present work investigates the capability of bottom-up coarse-graining (CG) methods for accurately modeling both structural and thermodynamic properties of all-atom (AA) models for molecular liquids. In particular, we consider 1, 2, and 3-site CG models for heptane, as well as 1 and 3-site CG models for toluene. For each model, we employ the multiscale coarse-graining method to determine interaction potentials that optimally approximate the configuration dependence of the many-body potential of mean force (PMF). We employ a previously developed "pressure-matching" variational principle to determine a volume-dependent contribution to the potential, UV(V), that approximates the volume-dependence of the PMF. We demonstrate that the resulting CG models describe AA density fluctuations with qualitative, but not quantitative, accuracy. Accordingly, we develop a self-consistent approach for further optimizing UV, such that the CG models accurately reproduce the equilibrium density, compressibility, and average pressure of the AA models, although the CG models still significantly underestimate the atomic pressure fluctuations. Additionally, by comparing this array of models that accurately describe the structure and thermodynamic pressure of heptane and toluene at a range of different resolutions, we investigate the impact of bottom-up coarse-graining upon thermodynamic properties. In particular, we demonstrate that UV accounts for the reduced cohesion in the CG models. Finally, we observe that bottom-up coarse-graining introduces subtle correlations between the resolution, the cohesive energy density, and the "simplicity" of the model.

Effective interaction potentials for model amphiphilic surfactants adsorbed at fluid–fluid interfaces

“…Coarse-graining approaches often provide less reliable thermodynamic descriptions compared to structural properties. Recent developments addresses this issue within an isothermal-isobaric ensemble, and it would be interesting to apply the corresponding extended CG scheme 60 to the present case to improve the surface pressure estimation in our CG systems. CG interaction potentials obtained from MS-CG can be successful in predicting static properties.…”

Determining Optimal Coarse‐Grained Representation for Biomolecules Using Internal Cluster Validation Indexes

“…To solve this problem, many researchers have devoted to developing the so‐called coarse‐grained (CG) models for accelerating simulation. The CG models could be constructed from the fine‐grained models such as all‐atom model by using the “bottom‐up” strategies . By resorting to the strategies, we could set up a connection between the statistical properties of fine‐grained ensembles and CG ensembles .…”

“…The CG models could be constructed from the fine-grained models such as all-atom model by using the "bottom-up" strategies. [9,10] By resorting to the strategies, we could set up a connection between the statistical properties of fine-grained ensembles and CG ensembles. [11][12][13][14][15][16][17][18][19][20][21] Construction of CG models based on all-atom models needs a preliminary definition of how to map fine-grained models to CG models.…”

Coarse-graining simulation approaches for polymer melts: the effect of potential range on computational efficiency

“…The target property can be defined in atomistic simulations that need to be performed at the start, in the so-called bottom-up approaches, 4,6,[22][23][24][25][26] or from experimental data in top-down CG models. 27,28 Hybrid approaches, which combine both bottom-up and top-down strategies have also been developed.…”