{
  "abstract": "Enhanced-sampling molecular dynamics is indispensable for studying biomolecular processes beyond the reach of conventional simulation, yet its reliability in realistic biological settings remains poorly characterized. Here, we compare four widely used approaches—replica-exchange umbrella sampling (REUS), well-tempered metadynamics (WT-MtD), well-tempered metadynamics–extended adaptive-biasing force (WTM-eABF), and on-the-fly probability enhanced sampling (OPES)—across five experimentally grounded processes: ligand binding, conformational change, kinase activation, membrane permeation, and ion conduction. Three findings emerge. Method performance does not transfer across biological contexts; each approach exhibits characteristic failure modes invisible in low-dimensional model systems but consequential in realistic landscapes. Self-consistency metrics, the field’s standard convergence diagnostic, are insufficient: simulations can satisfy convergence criteria while yielding quantitatively incorrect free-energy profiles. Cross-method agreement against an independent reference is therefore necessary. These results re-frame method selection as a context-dependent decision and argue that cross-method validation should become a community standard. Enhanced-sampling molecular dynamics methods are widely used to probe biomolecular processes, yet their reliability in realistic biological systems remains poorly characterized. This study shows that method performance does not transfer across biological contexts, that standard convergence metrics can be misleading, and that reliable free-energy estimation requires cross-method validation, underscoring the need for context-aware method selection.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA",
    "Laboratoire de Physique et Chimie Théoriques, Unité Mixte de Recherche no 7019, Université de Lorraine, Vandœuvre-lès-Nancy Cedex, France",
    "Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, College of Chemistry, Nankai University, Tianjin, PR China",
    "School of Physics, Georgia Institute of Technology, Atlanta, GA, USA",
    "Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA",
    "Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA",
    "Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA",
    "Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, USA",
    "Department of Chemistry, The University of Hawai'i at Mānoa, Honolulu, HI, USA",
    "Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA",
    "Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA. chipot@uchicago.edu",
    "Department of Chemistry, The University of Hawai'i at Mānoa, Honolulu, HI, USA. chipot@uchicago.edu",
    "Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA. chipot@uchicago.edu",
    "Laboratoire de Physique et Chimie Théoriques, Unité Mixte de Recherche no 7019, Université de Lorraine, Vandœuvre-lès-Nancy Cedex, France. chipot@uchicago.edu",
    "Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. chipot@uchicago.edu"
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 15,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Christopher Kang",
      "orcid": "0000-0002-9245-8101"
    },
    {
      "affs": [
        1
      ],
      "name": "Cheng Giuseppe Chen",
      "orcid": "0000-0003-3553-4718"
    },
    {
      "affs": [
        1
      ],
      "name": "Chenyu Tang",
      "orcid": "0000-0002-6914-7348"
    },
    {
      "affs": [
        1
      ],
      "name": "Sergio Contreras Arredondo",
      "orcid": "0009-0006-0428-4962"
    },
    {
      "affs": [
        2
      ],
      "name": "Mengchen Zhou",
      "orcid": "0009-0004-0489-9815"
    },
    {
      "affs": [
        2
      ],
      "name": "Haohao Fu",
      "orcid": "0000-0003-0908-0046"
    },
    {
      "affs": [
        3
      ],
      "name": "Lan Yang",
      "orcid": "0000-0002-8664-8929"
    },
    {
      "affs": [
        3
      ],
      "name": "James C. Gumbart",
      "orcid": "0000-0002-1510-7842"
    },
    {
      "affs": [
        4,
        5,
        6
      ],
      "name": "Ashkan Fakharzadeh",
      "orcid": "0009-0006-9598-1973"
    },
    {
      "affs": [
        7
      ],
      "name": "Mahmoud Moradi",
      "orcid": "0000-0002-0601-402X"
    },
    {
      "affs": [
        6
      ],
      "name": "Haochuan Chen",
      "orcid": "0000-0001-6447-1096"
    },
    {
      "affs": [
        8
      ],
      "name": "Rui Sun",
      "orcid": "0000-0003-0638-1353"
    },
    {
      "affs": [
        9
      ],
      "name": "Jonathan D Harris"
    },
    {
      "affs": [
        9
      ],
      "name": "Benoı̂t Roux",
      "orcid": "0000-0002-5254-2712"
    },
    {
      "affs": [
        10,
        11,
        12,
        13,
        14
      ],
      "name": "Christophe J. Chipot",
      "orcid": "0000-0002-9122-1698"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/5q224s97085zc.bib",
  "cited_by": 9,
  "doi": "10.1038/s41467-026-74165-y",
  "fulltext_url": null,
  "id": "5q224s97085zc",
  "issns": [
    "2041-1723"
  ],
  "landing_url": "https://doi.org/10.1038/s41467-026-74165-y",
  "language": "en",
  "licence": "CC-BY-NC-ND",
  "licence_label": "CC BY-NC-ND",
  "licence_source": "journal",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
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      "openalex",
      "1312|Protein Structure and Dynamics"
    ]
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  "openalex": "W7164525968",
  "pdf_url": null,
  "pmcid": "PMC13373210",
  "pmid": "42285925",
  "published": "2026-06-12",
  "publisher": "Nature Portfolio",
  "ris": "https://research.draconitic.com/paper/5q224s97085zc.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T13:26:48Z",
      "native_id": "W7164525968",
      "source": "openalex",
      "url": "https://doi.org/10.1038/s41467-026-74165-y"
    }
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  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Protein Structure and Dynamics",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Convergence is not correctness: context-dependent performance of enhanced-sampling methods across biological complexity",
  "title_text": "Convergence is not correctness: context-dependent performance of enhanced-sampling methods across biological complexity",
  "type": "peer-reviewed",
  "updated_at": "2026-11-08T13:20:43Z",
  "url": "https://research.draconitic.com/paper/5q224s97085zc",
  "venue": "Nature Communications",
  "versions": []
}