<i>PolyConstruct</i>: Adapting Biomolecular Simulation Pipelines for Polymers with <i>PolyBuild</i>, <i>PolyConf</i>, and <i>PolyTop</i>

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 <i>PolyConstruct</i>, a generalizable computational framework that leverages the GROMACS biomolecular simulation package for force field agnostic atomistic simulations of biocompatible and stimuli-responsive polymers. <i>PolyConstruct</i> contains three workflows, <i>PolyBuild</i>, <i>PolyTop</i>, and <i>PolyConf</i>, 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 <i>PolyBuild</i>, <i>PolyTop</i>, and <i>PolyConf</i> with examples of linear, branched, star, and dendritic polymers.