Progress toward a better BOCS: Systematic coarse-graining with local density potentials

Abstract

We describe version 5.0 of the Bottom-up Open-source Coarse-graining Software (BOCS) package. BOCS employs the force-matching variational principle to parameterize potentials for coarse-grained (CG) models directly from atomically detailed simulations. BOCS version 5.0 significantly extends previous versions by treating potentials that depend upon the local density (LD) around each particle, as well as potentials that depend upon the square gradient (SG) of this local density. We also describe a new package, PKG-BOCS, for simulating these potentials in LAMMPS. This software treats complex molecular topologies and provides considerable flexibility for defining the local density, as well as the LD and SG potentials. We present numerical calculations that provide physical insight into these potentials and demonstrate the accuracy of our implementation. Finally, we demonstrate that LD potentials can significantly improve the structural fidelity, thermodynamic properties, and transferability of CG models for water.