{
  "abstract": "gmx_MMPBSA is an end-to-end tool for performing end-state binding free energy calculations. Here, we present advances in the gmx_MMPBSA suite that simplify preparation, expand the calculation options, and improve the analysis of results. The new features include the GBNSR6 and nonlinear PB models, second-order cumulant (C2) entropy estimation, inclusion of explicit structural waters, and multiple alanine/glycine mutations. We also introduce amber_MMPBSA, a new entry point that accepts native AMBER input files and extends the calculation and analysis capabilities of gmx_MMPBSA to AMBER users. The redesigned graphical analyzer, gmx_MMPBSA_ana, and modernized Python API facilitate exploration of large datasets and comparisons across multiple systems. We illustrate the new gmx_MMPBSA capabilities using a diverse set of biomolecular complexes (protein-protein, protein-RNA, protein-small molecule, DNA-small molecule) and show how the calculated binding energies vary across systems depending on the methodological choices. The source code is available at https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 5,
  "authors": [
    {
      "name": "M. E. Valdes-Tresanco"
    },
    {
      "name": "M. S. Valdes-Tresanco"
    },
    {
      "name": "G. Romero-Hernandez"
    },
    {
      "name": "P. A. Valiente"
    },
    {
      "name": "E. Moreno"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/916bp2twmn7sj.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.10.24.761505",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.10.24.761505v1.full",
  "id": "916bp2twmn7sj",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.10.24.761505v1",
  "language": null,
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "bioinformatics"
    ],
    [
      "openalex",
      "1312|Protein Structure and Dynamics"
    ]
  ],
  "openalex": "W7223562597",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.10.24.761505v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-24",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/916bp2twmn7sj.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:29:34Z",
      "native_id": "10.64898/2026.10.24.761505",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.10.24.761505v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:bioinformatics",
      "subfield": "bioinformatics"
    }
  ],
  "title": "Expanding gmx_MMPBSA capabilities for end-state binding free energy calculations with GROMACS and AMBER",
  "title_text": "Expanding gmx_MMPBSA capabilities for end-state binding free energy calculations with GROMACS and AMBER",
  "type": "preprint",
  "updated_at": "2026-10-30T12:29:34Z",
  "url": "https://research.draconitic.com/paper/916bp2twmn7sj",
  "venue": "bioRxiv",
  "versions": []
}