MiMiCPy-FM: Una herramienta fácil de usar de coincidencia de fuerzas para extender la escala de tiempo de las...

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.