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Cited by 136Protein Structure and DynamicsAdvanced Physical and Chemical Molecular InteractionsAdvanced Chemical Physics Studies

CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed

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Hwang, Wonmuk, Austin, Steven L., Blondel, Arnaud, Boittier, Eric D., Boresch, Stefan, Buck, Matthias, Buckner, Joshua, Caflisch, Amedeo +65 more·2024·The Journal of Physical Chemistry B
DOI 10.1021/acs.jpcb.4c04100PMC PMC11492285
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Abstract

Since its inception nearly a half century ago, CHARMM has been playing a central role in computational biochemistry and biophysics. Commensurate with the developments in experimental research and advances in computer hardware, the range of methods and applicability of CHARMM have also grown. This review summarizes major developments that occurred after 2009 when the last review of CHARMM was published. They include the following: new faster simulation engines, accessible user interfaces for convenient workflows, and a vast array of simulation and analysis methods that encompass quantum mechanical, atomistic, and coarse-grained levels, as well as extensive coverage of force fields. In addition to providing the current snapshot of the CHARMM development, this review may serve as a starting point for exploring relevant theories and computational methods for tackling contemporary and emerging problems in biomolecular systems. CHARMM is freely available for academic and nonprofit research at https://academiccharmm.org/program.

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  • One of the most powerful aspects of all-atom molecular dynamics is the transferability of the force fields to make predictions about interactions between molecules.

    “One of the most powerful aspects of all-atom molecular dynamics is the transferability of the force fields to make predictions about interactions between molecules.54”

    From Bringing the genetically minimal cell to life on a computer in 4D (2026) · cites this paper as [54]

    The ‘Small Molecules’ section (page unavailable) describes assigning force-field parameters across compounds and reports successful validation on drug-like molecules, supporting the predictive use of force fields. But the paper’s explicit claim of high transferability concerns PRIMO, a coarse-grained model, rather than all-atom molecular dynamics; it does not establish transferability as one of all-atom MD’s most powerful aspects. (LLM, conf=0.78)

    Experimental — accuracy not yet measured

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Authors
Hwang, W., Austin, S. L., Blondel, A., Boittier, E. D., Boresch, S., Buck, M., Buckner, J., Caflisch, A., Chang, H.-T., Cheng, X., Choi, Y. K., Chu, J.-W., Crowley, M. F., Cui, Q., Damjanovic, A., Deng, Y., Devereux, M., Ding, X., Feig, M. F., Gao, J., Glowacki, D. R., Gonzales, J. E., Hamaneh, M. B., Harder, E. D., Hayes, R. L., Huang, J., Huang, Y., Hudson, P. S., Im, W., Islam, S. M., Jiang, W., Jones, M. R., Käser, S., Kearns, F. L., Kern, N. R., Klauda, J. B., Lazaridis, T., Lee, J., Lemkul, J. A., Liu, X., Luo, Y., MacKerell, A. D., Major, D. T., Meuwly, M., Nam, K., Nilsson, L., Ovchinnikov, V., Paci, E., Park, S., Pastor, R. W., Pittman, A. R., Post, C. B., Prasad, S., Pu, J., Qi, Y., Rathinavelan, T., Roe, D. R., Roux, B., Rowley, C. N., Shen, J., Simmonett, A. C., Sodt, A. J., Töpfer, K., Upadhyay, M., van der Vaart, A., Vazquez-Salazar, L. I., Venable, R. M., Warrensford, L. C., Woodcock, H. L., Wu, Y., Brooks, C. L., Brooks, B. R., & Karplus, M.
Affiliations
  • Korea Institute for Advanced Study (KR)
  • University of South Florida (US)
  • Centre National de la Recherche Scientifique (FR)
  • University of Basel (CH)
  • University of Vienna (AT)
  • Case Western Reserve University (US)
  • University of Michigan (US)
  • University of Zurich (CH)
  • National Yang Ming Chiao Tung University (TW)
  • Chinese Academy of Sciences (CN)
  • Lehigh University (US)
  • National Laboratory of the Rockies (US)
  • Boston University (US)
  • National Institutes of Health (US)
  • Shanghai R&D Center, DP Technology, Ltd., Shanghai 201210, China
  • Tufts University (US)
  • Michigan State University (US)
  • University of Minnesota (US)
  • Universidade de Santiago de Compostela (ES)
  • Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106, United States
  • Schrodinger (United States) (US)
  • University of California, Irvine (US)
  • Westlake University (CN)
  • Jimei University (CN)
  • Pfizer (United States) (US)
  • Delaware State University (US)
  • Argonne National Laboratory (US)
  • University of Maryland, College Park (US)
  • City College of New York (US)
  • Korea Research Institute of Bioscience and Biotechnology (KR)
  • Virginia Tech (US)
  • Western University of Health Sciences (US)
  • University of Maryland, Baltimore (US)
  • Bar-Ilan University (IL)
  • The University of Texas at Arlington (US)
  • Karolinska Institutet (SE)
  • Harvard University (US)
  • University of Bologna (IT)
  • Purdue University West Lafayette (US)
  • Indiana University Indianapolis (US)
  • Fudan University (CN)
  • Indian Institute of Technology Hyderabad (IN)
  • Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
  • Carleton University (CA)
  • Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
Corresponding author
  • Hwang, Wonmuk
  • Brooks, Charles L.
  • Brooks, Bernard R.
ORCID
Venue
The Journal of Physical Chemistry B
Publisher
American Chemical Society (ACS)
Published
2024-09-20
Volume
128
Issue
41
Pages
9976-10042
ISSN
  • 1520-5207 (ISSN-L)
  • 1520-6106
DOI
10.1021/acs.jpcb.4c04100
PMC
PMC11492285
OpenAlex
W4402681508
Cited by
136
References
734
Citations by year
2026: 73 · 2025: 54 · 2024: 9
FWCI
5.56
Type
journal article
Language
en
Open access
Licence
Locations
  • The Journal of Physical Chemistry B (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • VTechWorks (Virginia Tech) (publishedVersion, cc-by)
  • HAL (submittedVersion, cc-by)
  • Archivio istituzionale della ricerca (Alma Mater Studiorum Università di Bologna) (submittedVersion, cc-by)
  • eScholarship (California Digital Library) (submittedVersion, cc-by)
  • OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
  • IUScholarWorks (Indiana University) (submittedVersion, cc-by)
  • Knowledge@UChicago (University of Chicago) (submittedVersion)
  • Zurich Open Repository and Archive (University of Zurich) (submittedVersion, cc-by)
Funders
  • NCCR Catalysis
  • European Research Council (866559)
  • Schweizerischer Nationalfonds zur F?rderung der Wissenschaftlichen Forschung (200020-188724, 310030-212195)
  • U.S. National Library of Medicine
  • Office of Science (DE-AC02-06CH11357)
  • Universit?t Basel
  • National Institutes of Health (R01GM039478, R01GM046736, R01GM129519, R01GM132481, R01GM135392, R01GM138472, R01GM140316, R01GM143810, R21GM148895, R35GM126948, R35GM131710, R35GM137058, R35GM141930, R35GM148261, ZIA HL000340, ZIA HL001051, ZIA HL001052)
  • National Science Foundation (MCB-1855942, MCB-1919096, MCB-211172)
  • National Science and Technology Council (112-2113-M-A49-018-MY3)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
  • Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Advanced Chemical Physics Studies
Keywords
CHARMM, molecular dynamics simulation, simulation engine, user interface, force fields, quantum mechanical methods, atomistic simulation, coarse-grained simulation, biomolecular systems, computational biophysics
MeSH terms
Quantum Theory, Software, Molecular Dynamics Simulation

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

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