PolyConstruct: Adapting Biomolecular Simulation Pipelines for Polymers with PolyBuild, PolyConf, and PolyTop.

Abstract

Molecular dynamics simulations are invaluable tools that provide both a molecular understanding and a means for the rational design of polymers. A key bottleneck in current polymer molecular dynamics simulations is the lack of a comprehensive and generalizable method that streamlines the preparation of simulations for novel polymer architectures and chemistries. Here, we present PolyConstruct, a generalizable computational framework that leverages the GROMACS biomolecular simulation package for force field agnostic atomistic simulations of biocompatible and stimuli-responsive polymers. PolyConstruct contains three workflows, PolyBuild, PolyTop, and PolyConf, for generating chemically accurate topology parameters from monomer parameters and structural coordinates for complex polymer architectures and chemistries. We highlight the utility and robustness of PolyBuild, PolyTop, and PolyConf with examples of linear, branched, star, and dendritic polymers.