Coarse graining of nonbonded inter-particle potentials using automatic simplex optimization to fit structural properties

Abstract

We implemented a coarse-graining procedure to construct mesoscopic models of complex molecules. The final aim is to obtain better results on properties depending on slow modes of the molecules. Therefore the number of particles considered in molecular dynamics simulations is reduced while conserving as many properties of the original substance as possible. We address the problem of finding nonbonded interaction parameters which reproduce structural properties from experiment or atomistic simulations. The approach consists of optimizing automatically nonbonded parameters using the simplex algorithm to fit structural properties like the radial distribution function as target functions. Moreover, any mix of structural and thermodynamic properties can be included in the target function. Different spherically symmetric inter-particle potentials are discussed. Besides demonstrating the method for Lennard-Jones liquids, it is applied to several more complex molecular liquids such as diphenyl carbonate, tetrahydrofurane, and monomers of poly(isoprene).

Challenges in Multiscale Modeling of Polymer Dynamics

“…If the method aims to reproduce the target pair distribution functions given by the all-atomistic simulations, then it is structure-based. The structure-based methods include the iterative Boltzmann inversion (IBI) method [82,83], the Kirkwood-Buff IBI method [164], the inverse Monte Carlo (IMC) method [165], the relative entropy method [166] and the generalized Yvon-Born-Green theory [167]. All structure-based methods follow the IBI method in spirit, but with different optimization or mapping schemes.…”

“…According to the canonical equilibrium distribution function [175], the configurational probability distribution of atomic positions, r n , for the all-atomistic model at given volume, V , and temperature, T , is [82,83]:…”

“…From the above equation, it is clear that the derived coarse-grained potential function, U (R N ), is not a conventional potential energy function [82,83,176,177]. The potential function, U (R N ), contains many-body effects and highly depends on the configurational free energy function or potential of mean force (PMF) of the thermodynamic state point.…”

Nonperiodic stochastic boundary conditions for molecular dynamics simulations of materials embedded into a continuum mechanics domain

“…34,35 The advantage of using anchor points instead of space-fixing all or a subset of the atoms is that the force on the anchor point comes only from a simple harmonic potential. There are no many-body or curvilinear terms (bond angle and dihedral forces) 1 and no complex analytical 39 or tabulated numerical potentials 40,41 involved here. All these complicated interactions are allowed exclusively between particles, but not between particles and anchor points.…”

Systematic comparison of force fields for microscopic simulations of NaCl in aqueous solutions: Diffusion, free energy of hydration, and structural properties

“…In contrast, structural properties without known experimental values vary significantly between force fields. This uncertainty has become a significant problem recently since structural prop-erties are essential in force field development for coarsegrained systems [20,21].…”