Journal Article

FZJ-2026-01873

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png MiMiCPy-FM: A User-Friendly Force Matching Tool for Extending the Time Scale of QM/MM MD MiMiC Simulations

Shivakumar, S. (First author)FZJ* ; Frumenzio, G. (First author) ; Musiani, F. ; Affinito, F. ; Ippoliti, E.FZJ* ; Raghavan, B. ; Rossetti, G.FZJ* ; Mandelli, D. (Corresponding author)FZJ* ; Carloni, P. (Corresponding author)FZJ*

2026
American Chemical Society Washington, DC

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Please use a persistent id in citations: doi:10.1021/acs.jcim.5c03185  doi:10.34734/FZJ-2026-01873

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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Contributing Institute(s):

1. Computational Biomedicine (INM-9)

Research Program(s):

1. 899 - ohne Topic (POF4-899) (POF4-899)

Appears in the scientific report 2026

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Database coverage:
; ; ; Clarivate Analytics Master Journal List ; Current Contents - Physical, Chemical and Earth Sciences ; Essential Science Indicators ; IF >= 5 ; JCR ; SCOPUS ; Science Citation Index Expanded ; Web of Science Core Collection

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