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MiMiCPy-FM: A User-Friendly Force Matching Tool for Extending the Time Scale of QM/MM MD MiMiC Simulations
KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab. Computational Biomedicine (INM-9), Forschungszentrum Jülich, Jülich 52428, Germany; Department of Physics, RWTH Aachen University, Aachen 52062, Germany.
CINECA, Casalecchio di Reno 40033, Italy; Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy.
Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy.ORCID iD: 0000-0003-0200-1712
CINECA, Casalecchio di Reno 40033, Italy.
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2026 (English)In: Journal of Chemical Information and Modeling, ISSN 1549-9596, E-ISSN 1549-960X, Vol. 66, no 5, p. 2458-2465Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
American Chemical Society (ACS) , 2026. Vol. 66, no 5, p. 2458-2465
National Category
Theoretical Chemistry Physical Chemistry Biophysics
Identifiers
URN: urn:nbn:se:kth:diva-378604DOI: 10.1021/acs.jcim.5c03185ISI: 001696655500001PubMedID: 41717765Scopus ID: 2-s2.0-105032051580OAI: oai:DiVA.org:kth-378604DiVA, id: diva2:2048400
Note

QC 20260325

Available from: 2026-03-25 Created: 2026-03-25 Last updated: 2026-03-25Bibliographically approved

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Shivakumar, Sachin

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