{
  "abstract": "Constant pH molecular dynamics (CpHMD) has emerged as a powerful method for simulating pH-dependent processes in proteins and other biomolecules. The original implementation of the PME-based CpHMD in the GROMACS software included the CHARMM36 and Martini 2 force fields for the treatment of the titratable amino acids in proteins. As requested by the user community, this work contains the parametrization of titratable residues for the Amber99sb-ildn, Amber14sb, and OPLS-AA/M force fields. In addition to carefully carrying out the parametrization process, the performance of the different force fields in the scope of CpHMD is evaluated by performing computational titrations for a set of benchmark proteins. The calculated pKa values obtained using all force fields yield an average root-mean-square error of about 1 pH unit in comparison to experimental pKa values, which is in line with previous CpHMD benchmarks. The presented work expands the applicability of the PME-based CpHMD method in GROMACS and guides the researchers aiming to perform accurate and efficient CpHMD simulations.",
  "abstract_shown": true,
  "affiliations": [
    "Computational Physics Laboratory, Tampere University, 33720Tampere, Finland.",
    "Theoretical Physics and Center for Biophysics, Saarland University, 66123Saarbrücken, Germany."
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 1,
  "authors": [
    {
      "affs": [
        0,
        1
      ],
      "name": "Noora Aho",
      "orcid": "0009-0008-1243-0215"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/32a1p09k5hsjs.bib",
  "cited_by": 0,
  "doi": "10.1021/acs.jctc.6c00678",
  "fulltext_url": "https://europepmc.org/articles/PMC13602905",
  "id": "32a1p09k5hsjs",
  "issns": [
    "1549-9618",
    "1549-9626"
  ],
  "landing_url": "https://europepmc.org/article/MED/42917451",
  "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",
      "1312|Protein Structure and Dynamics"
    ]
  ],
  "openalex": "W7170475135",
  "pdf_url": "https://europepmc.org/articles/PMC13602905?pdf=render",
  "pmcid": "PMC13602905",
  "pmid": "42917451",
  "published": "2026-09-01",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/32a1p09k5hsjs.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:21:02Z",
      "native_id": "MED:42917451",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42917451"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Protein Structure and Dynamics",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Protein Titration Benchmark of CHARMM36, Amber99sb-ildn, Amber14sb, OPLS-AA/M, and Martini 2 Force Fields for Constant pH Molecular Dynamics in GROMACS.",
  "title_text": "Protein Titration Benchmark of CHARMM36, Amber99sb-ildn, Amber14sb, OPLS-AA/M, and Martini 2 Force Fields for Constant pH Molecular Dynamics in GROMACS.",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:21:02Z",
  "url": "https://research.draconitic.com/paper/32a1p09k5hsjs",
  "venue": "Journal of chemical theory and computation",
  "versions": []
}