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

TL;DR

MiMiCPy-FM is a tool that extends the time scale of QM/MM simulations by automatically generating force fields for classical MD simulations.

Contribution

MiMiCPy-FM introduces a user-friendly, automated force matching tool integrated with the MiMiC interface for QM/MM simulations.

Findings

MiMiCPy-FM supports systems with and without covalent QM/MM boundaries.

The tool generates updated topology files compatible with GROMACS for classical MD simulations.

An application to a Mg-based enzyme demonstrates its effectiveness in transitioning to long-time scale simulations.

Abstract

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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