Several industrial and commercial applications rely on designing cross-linked polymers with targeted properties. To achieve the target properties, understanding the underlying structure-property relationships in these polymers is necessary. Molecular simulations have emerged as important tools to investigate the correlation between the microscopic structure and dynamics with polymer properties. To perform molecular simulations, an initial structure of the cross-linked polymer is required. However, it is challenging to determine the structure of amorphous and cross-linked polymers at the desired conditions. To address the challenge of generating the intial structure of the polymers without a well-defined structure, various bespoke polymerization protocols have been developed and are implemented in different software. However, given the growing need for Transparent, Reproducible, Usable by others, and Extensible (TRUE)[1] molecular simulations, it is critical to have a simple and generalized tool supporting any bespoke polymerization protocol. To advance the study of cross-linked polymers using molecular simulations, we have developed an open-source and generalizable standalone Python-based software, PolyPlex, for constructing an all-atom polymer structure using GROMACS as the molecular simulations engine. The generalizability and extendibility of the software are demonstrated through two cross-linked polymers — polyamide and epoxy. For polyamide, the polymerization protocol developed by Kolev and Freger[2] was implemented. Epoxy was generated using the protocol proposed by Demir and Walsh[3]. In our presentation, we report the code architecture, test cases of the building blocks of the reported polymerization protocols, and comparison of properties of generated polymer structures with experiments to illustrate the scope and applicability to various polymer researchers. We envision that users will easily be able to add new features and use existing features to contribute new protocols to the software. We expect that PolyPlex will be widely adapted by the community and will contribute to the growth of molecular simulation studies of cross-linked polymers.

Polyplex: A generalized and open-source Python software for generating all-atom cross-linked polymer structures

ACS Fall 2021

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