Fitting coarse-grained distribution functions through an iterative force-matching method

Abstract

An iterative coarse-graining method is developed for systematically converting an atomistic force field to a model at lower resolution that is able to accurately reproduce the distribution functions defined in the coarse-grained potential. The method starts from the multiscale coarse-graining (MS-CG) approach, and it iteratively refines the distribution functions using repeated applications of the MS-CG algorithm. It is justified on the basis of the force matching normal equation, which can be considered a discrete form of the Yvon-Born-Green equation in liquid state theory. Numerical results for molecular systems involving pairwise nonbonded and three-body bonded interactions are obtained, and comparison with other approaches in literature is provided.

An analysis of wavelet frame based scattered data reconstruction

“…The simulation time step is set to 2 fs. The force matching method [34,31] was applied to the atomistic configurations to generate the CG potentials, and 10 ns of the trajectory was used for analysis.…”

“…It finds applications in various fields, for instance, terrain modeling, surface reconstruction and the numerical solution of partial differential equations, see e.g., [39]. Moreover, it can be used to approximate sparse range data [24], and it can be even applied to fit coarse-grained force functions in structural biology [34,31], as we will learn below.…”

From Atomistic to Systematic Coarse-Grained Models for Molecular Systems

“…Possible reasons for these discrepancies are related to the fact that FM and RE are only asymptotically equivalent, meaning that finite size basis sets effects might be important during the numerical optimization procedure. Clearly more work is required in order to clarify such differences [19,9,10].…”

Perspective: Reaches of chemical physics in biology

“…34 However, only recently rigorous methods for devising CG models have been developed. Lu et al 35 have used force-matching method to construct CG potentials that reproduce distribution functions obtained in detailed simulations using a formalism based on Yuon-Born-Green equations familiar in the context of classical many body systems.…”