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Peer-reviewedCC BYJournal of chemical information and modeling

Seamless QM/MM Simulations via a GROMACS-CP2K Interface.

  • Dmitry Morozov1
  • Christian Blau2
  • Ole Schütt3
  • Vladimir Mironov4
  • Arno Proeme5
  • Holly Judge5
  • Thomas D Kühne6,7,8
  • Berk Hess2
  • Gerrit Groenhof1
8 affiliations
  1. 1Nanoscience Center and Department of Chemistry, University of Jyväskylä, P.O. Box 35, JyväskyläFI-40014, Finland.
  2. 2Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, SolnaSE-17165, Sweden.
  3. 3CP2K Foundation, ZürichCH-8057, Switzerland.
  4. 4Terra Quantum AG , Kornhausstrasse 25, St. GallenCH-9000, Switzerland.
  5. 5EPCC, The University of Edinburgh, Bayes Centre , 47 Potterrow, EdinburghEH8 9BT, U.K.
  6. 6Center for Advanced Systems Understanding (CASUS) , Untermarkt 20, Görlitz02826, Germany.
  7. 7Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Bautzner Landstraße 400, Dresden01328, Germany.
  8. 8Institute of Artificial Intelligence, Technische Universität Dresden, Helmholtzstraße 10, Dresden01069, Germany.
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Abstract

Understanding and controlling chemical reactivity in biological systems require atomic-level insight into processes that are often inaccessible to experiments. Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations provide a powerful framework for describing chemical reactions in complex environments, but their practical application remains limited by fragmented software ecosystems, restricted accessibility, and methodological approximations that can compromise accuracy and reproducibility. In particular, many existing QM/MM implementations rely on ad hoc couplings, proprietary software, or truncated treatments of long-range electrostatic interactions. Here, we present a robust and fully periodic QM/MM interface between the open-source molecular dynamics engine GROMACS and the electronic structure theory code CP2K. The implementation enables efficient and reproducible QM/MM molecular dynamics and enhanced sampling simulations with a consistent treatment of long-range electrostatics under periodic boundary conditions. By combining the strengths of two widely used community codes, this interface provides a general and scalable platform for studying chemical reactivity in biological systems and establishes a transparent reference implementation for QM/MM simulations.

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Cite

BibTeXRIS
BibTeX
@article{morozov2026seamless,
  title = {{Seamless QM/MM Simulations via a GROMACS-CP2K Interface.}},
  author = {Dmitry Morozov and Christian Blau and Ole Schütt and Vladimir Mironov and Arno Proeme and Holly Judge and Thomas D Kühne and Berk Hess and Gerrit Groenhof},
  journal = {Journal of chemical information and modeling},
  year = {2026},
  month = sep,
  doi = {10.1021/acs.jcim.6c02073},
  url = {https://europepmc.org/article/MED/42906049},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - Seamless QM/MM Simulations via a GROMACS-CP2K Interface.
AU  - Dmitry Morozov
AU  - Christian Blau
AU  - Ole Schütt
AU  - Vladimir Mironov
AU  - Arno Proeme
AU  - Holly Judge
AU  - Thomas D Kühne
AU  - Berk Hess
AU  - Gerrit Groenhof
PY  - 2026
DA  - 2026/09/01
JO  - Journal of chemical information and modeling
DO  - 10.1021/acs.jcim.6c02073
UR  - https://europepmc.org/article/MED/42906049
AB  - Understanding and controlling chemical reactivity in biological systems require atomic-level insight into processes that are often inaccessible to experiments. Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations provide a powerful framework for describing chemical reactions in complex environments, but their practical application remains limited by fragmented software ecosystems, restricted accessibility, and methodological approximations that can compromise accuracy and reproducibility. In particular, many existing QM/MM implementations rely on ad hoc couplings, proprietary software, or truncated treatments of long-range electrostatic interactions. Here, we present a robust and fully periodic QM/MM interface between the open-source molecular dynamics engine GROMACS and the electronic structure theory code CP2K. The implementation enables efficient and reproducible QM/MM molecular dynamics and enhanced sampling simulations with a consistent treatment of long-range electrostatics under periodic boundary conditions. By combining the strengths of two widely used community codes, this interface provides a general and scalable platform for studying chemical reactivity in biological systems and establishes a transparent reference implementation for QM/MM simulations.
SN  - 1549-9596
SN  - 1549-960X
ER  -