A Multi-Scale Molecular Dynamics Scheme/Toolkit for Polymer Modeling

Multi-scale modeling of polymer systems remains a fundamental challenge in materials science due to the strongly coupled structures and dynamics across atomic, mesoscopic, and macroscopic scales. Here, we present PyGAMD-ChemFAST (Python GPU-accelerated Molecular Dynamics - Chemical-Friendly Automated Simulation Toolkit), an integrated modeling and simulation framework that combines a molecular simulation platform with an automated modeling and processing toolkit. The framework supports bidirectional cross-scale modeling, integrating the mapping from all-atom (AA) to coarse-grained (CG) models in coarse-graining and from CG back to AA in fine-graining, while automating the entire workflow from model parameterization through dynamics simulation to property analysis. It accommodates complex polymer topologies and ensures cross-scale force field compatibility. By unifying modeling and simulation in a programmable environment, PyGAMD-ChemFAST enhances computational efficiency and ensures parameter consistency, especially in studying phase separation, glass transition, crystallization, and mechanical behavior. This integrated framework provides an efficient and reliable platform for high-throughput, multi-scale polymer research.