MiMiCPy-FM: A User-Friendly Force Matching Tool for Extending the Time Scale of QM/MM MD MiMiC Simulations

Le résumé fourni par la source

Force matching (FM) algorithms develop force fields to dramatically extend the time scales of quantum mechanical/molecular mechanics (QM/MM) molecular dynamics (MD) simulations. Here, we present MiMiCPy-FM, an implementation of the generalized QM/MM FM approach for the automated parametrization of biomolecular force fields. MiMiCPy-FM streamlines the optimization of force field parameters by using reference data generated by the recently developed, highly scalable QM/MM MD MiMiC interface. MiMiCPy-FM is fully integrated within the MiMiCPy framework, providing both a command-line interface for quick execution and a Python library for advanced, customizable workflows. The tool is able to treat systems with and without covalent QM/MM boundaries and produces updated topology files that can be directly used to perform classical MD simulations with GROMACS. An application to a complex Mg-based enzyme of pharmacological relevance illustrates how MiMiCPy-FM enables a seamless transition from MiMiC QM/MM MD simulations to long-time scale, force-matched classical MD simulations.

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