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Ongoing advances in force field and computer hardware development enable theuse of molecular dynamics (MD) to simulate increasingly complex systems withthe ultimate goal of reaching cellular complexity. At the same time, rationaldesign by high-throughput (HT) simulations is another forefront of MD. In theseareas, the Martini coarse-grained force field, especially the latest version(i.e. v3), is being actively explored because it offers enhancedspatial-temporal resolution. However, the automation tools for preparingsimulations with the Martini force field, accompanying the previous version,were not designed for HT simulations or studies of complex cellular systems.Therefore, they become a major limiting factor. To address these shortcomings,we present the open-source Vermouth python library. Vermouth is designed tobecome the unified framework for developing programs, which prepare, run, andanalyze Martini simulations of complex systems. To demonstrate the power of theVermouth library, the Martinize2 program is showcased as a generalization ofthe martinize script, originally aimed to set up simulations of proteins. Incontrast to the previous version, Martinize2 automatically handles protonationstates in proteins and post-translation modifications, offers more options tofine-tune structural biases such as the elastic network, and can convertnon-protein molecules such as ligands. Finally, Martinize2 is used in twohigh-complexity benchmarks. The entire I-TASSER protein template database aswell as a subset of 200,000 structures from the AlphaFold Protein StructureDatabase are converted to CG resolution and we illustrate how the checks oninput structure quality can safeguard high-throughput applications.

Martinize2 and Vermouth: Unified Framework for Topology Generation