{
  "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.",
  "abstract_shown": true,
  "affiliations": [
    "Nanoscience Center and Department of Chemistry, University of Jyväskylä, P.O. Box 35, JyväskyläFI-40014, Finland.",
    "Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, SolnaSE-17165, Sweden.",
    "CP2K Foundation, ZürichCH-8057, Switzerland.",
    "Terra Quantum AG , Kornhausstrasse 25, St. GallenCH-9000, Switzerland.",
    "EPCC, The University of Edinburgh, Bayes Centre , 47 Potterrow, EdinburghEH8 9BT, U.K.",
    "Center for Advanced Systems Understanding (CASUS) , Untermarkt 20, Görlitz02826, Germany.",
    "Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Bautzner Landstraße 400, Dresden01328, Germany.",
    "Institute of Artificial Intelligence, Technische Universität Dresden, Helmholtzstraße 10, Dresden01069, Germany."
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 9,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Dmitry Morozov",
      "orcid": "0000-0001-9524-948X"
    },
    {
      "affs": [
        1
      ],
      "name": "Christian Blau"
    },
    {
      "affs": [
        2
      ],
      "name": "Ole Schütt",
      "orcid": "0009-0005-8661-3418"
    },
    {
      "affs": [
        3
      ],
      "name": "Vladimir Mironov"
    },
    {
      "affs": [
        4
      ],
      "name": "Arno Proeme"
    },
    {
      "affs": [
        4
      ],
      "name": "Holly Judge"
    },
    {
      "affs": [
        5,
        6,
        7
      ],
      "name": "Thomas D Kühne",
      "orcid": "0000-0001-5471-2407"
    },
    {
      "affs": [
        1
      ],
      "name": "Berk Hess",
      "orcid": "0000-0002-7498-7763"
    },
    {
      "affs": [
        0
      ],
      "name": "Gerrit Groenhof",
      "orcid": "0000-0001-8148-5334"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/aakz8ze7a67yx.bib",
  "cited_by": 1,
  "doi": "10.1021/acs.jcim.6c02073",
  "fulltext_url": "https://europepmc.org/articles/PMC13625966",
  "id": "aakz8ze7a67yx",
  "issns": [
    "1549-9596",
    "1549-960X"
  ],
  "landing_url": "https://europepmc.org/article/MED/42906049",
  "language": "eng",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "3107|Advanced Chemical Physics Studies"
    ]
  ],
  "openalex": "W7212182484",
  "pdf_url": "https://europepmc.org/articles/PMC13625966?pdf=render",
  "pmcid": "PMC13625966",
  "pmid": "42906049",
  "published": "2026-09-01",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/aakz8ze7a67yx.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:19:57Z",
      "native_id": "MED:42906049",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42906049"
    }
  ],
  "subjects": [
    {
      "field": "physics",
      "origin": "openalex:3107|Advanced Chemical Physics Studies",
      "subfield": "amo"
    }
  ],
  "title": "Seamless QM/MM Simulations via a GROMACS-CP2K Interface.",
  "title_text": "Seamless QM/MM Simulations via a GROMACS-CP2K Interface.",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:19:57Z",
  "url": "https://research.draconitic.com/paper/aakz8ze7a67yx",
  "venue": "Journal of chemical information and modeling",
  "versions": [
    {
      "doi": "10.26434/chemrxiv.15005148/v2",
      "pid": "fcya9v6wrvgvv",
      "relation": "preprint",
      "title": "Seamless QM/MM simulations via a GROMACS–CP2K interface",
      "venue": "ChemRxiv"
    }
  ]
}