AA2UA: A Python tool for converting all-atom PDB models into their united atom coarse grained counterparts for use in LAMMPS

Abstract

Atomistic simulations are crucial for understanding material properties at the molecular level but are limited by high computational costs, especially for large, complex systems like bituminous materials. Our team developed a Force-matched United Atom (UA) Coarse Graining (CG) force field to enhance computational efficiency while retaining atomic detail. However, converting all-atom models to CG models is complex, requiring detailed atom-to-bead mapping and compatibility with molecular dynamics (MD) engines like LAMMPS. To address this, we introduce AA2UA, an open-source software that simplifies the conversion of PDB files into LAMMPS-readable structure topology files, facilitating broader use of the developed UA force field.