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CHARMM: The biomolecular simulation program

Authors

  • B. R. Brooks,

    Corresponding author
    1. Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
    • Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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  • C. L. Brooks III,

    Corresponding author
    1. Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
    2. Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109
    • Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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  • A. D. Mackerell Jr.,

    Corresponding author
    1. Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201
    • Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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  • L. Nilsson,

    Corresponding author
    1. Department of Biosciences and Nutrition, Karolinska Institutet, SE-141 57, Huddinge, Sweden
    • Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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  • R. J. Petrella,

    Corresponding author
    1. Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
    2. Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115
    • Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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  • B. Roux,

    Corresponding author
    1. Department of Biochemistry and Molecular Biology, University of Chicago, Gordon Center for Integrative Science, Chicago, Illinois 60637
    • Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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  • Y. Won,

    Corresponding author
    1. Department of Chemistry, Hanyang University, Seoul 133-792, Korea
    • Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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  • G. Archontis,

    1. Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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  • C. Bartels,

    1. Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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  • S. Boresch,

    1. Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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  • A. Caflisch,

    1. Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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  • L. Caves,

    1. Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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  • Q. Cui,

    1. Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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  • A. R. Dinner,

    1. Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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  • M. Feig,

    1. Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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  • S. Fischer,

    1. Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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  • J. Gao,

    1. Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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  • M. Hodoscek,

    1. Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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  • W. Im,

    1. Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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  • K. Kuczera,

    1. Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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  • T. Lazaridis,

    1. Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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  • J. Ma,

    1. Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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  • V. Ovchinnikov,

    1. Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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  • E. Paci,

    1. Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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  • R. W. Pastor,

    1. Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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  • C. B. Post,

    1. Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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  • J. Z. Pu,

    1. Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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  • M. Schaefer,

    1. Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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  • B. Tidor,

    1. Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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  • R. M. Venable,

    1. Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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  • H. L. Woodcock,

    1. Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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  • X. Wu,

    1. Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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  • W. Yang,

    1. Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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  • D. M. York,

    1. Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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  • M. Karplus

    Corresponding author
    1. Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
    2. Laboratoire de Chimie Biophysique, ISIS, Université de Strasbourg, 67000 Strasbourg, France
    • Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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Abstract

CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estimators, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numerous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983. © 2009 Wiley Periodicals, Inc.J Comput Chem, 2009.

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