Systematic Coarse-Grained Models for Molecular Systems Using Entropy
Open Access
- 22 November 2019
- conference paper
- conference paper
- Published by MDPI AG in Proceedings
- Vol. 46 (1), 27
- https://doi.org/10.3390/ecea-5-06710
Abstract
The development of systematic coarse-grained mesoscopic models for complex molecular systems is an intense research area. Here we first give an overview of different methods for obtaining optimal parametrized coarse-grained models, starting from detailed atomistic representation for high dimensional molecular systems. We focus on methods based on information theory, such as relative entropy, showing that they provide parameterizations of coarse-grained models at equilibrium by minimizing a fitting functional over a parameter space. We also connect them with structural-based (inverse Boltzmann) and force matching methods. All the methods mentioned in principle are employed to approximate a many-body potential, the (n-body) potential of mean force, describing the equilibrium distribution of coarse-grained sites observed in simulations of atomically detailed models. We also present in a mathematically consistent way the entropy and force matching methods and their equivalence, which we derive for general nonlinear coarse-graining maps. We apply, and compare, the above-described methodologies in several molecular systems: A simple fluid (methane), water and a polymer (polyethylene) bulk system. Finally, for the latter we also provide reliable confidence intervals using a statistical analysis resampling technique, the bootstrap method.Keywords
This publication has 14 references indexed in Scilit:
- Parametrizing coarse grained models for molecular systems at equilibriumThe European Physical Journal Special Topics, 2016
- Path-space variational inference for non-equilibrium coarse-grained systemsJournal of Computational Physics, 2016
- The geometry of generalized force matching and related information metrics in coarse-graining of molecular systemsThe Journal of Chemical Physics, 2015
- Information-theoretic tools for parametrized coarse-graining of non-equilibrium extended systemsThe Journal of Chemical Physics, 2013
- Coarse-graining entropy, forces, and structuresThe Journal of Chemical Physics, 2011
- Anomalous waterlike behavior in spherically-symmetric water models optimized with the relative entropyPhysical Chemistry Chemical Physics, 2009
- The relative entropy is fundamental to multiscale and inverse thermodynamic problemsThe Journal of Chemical Physics, 2008
- The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular modelsThe Journal of Chemical Physics, 2008
- Hierarchical Modeling of Polystyrene: From Atomistic to Coarse-Grained SimulationsMacromolecules, 2006
- Empirical potential Monte Carlo simulation of fluid structureChemical Physics, 1996