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10. CHARMM: the biomolecular simulation program

Author

Brooks, B. R., Brooks III, C. L., Mackerell Jr., A. D., Nilsson, L., Petrella, R. J., Roux, B., Won, Y., Archontis, Georgios Z., Bartels, C., Boresch, S., Caflisch, A., Caves, L., Cui, Q., Dinner, A. R., Feig, M., Fischer, S., Gao, J., Hodoscek, M., Im, W., Kuczera, K., Lazaridis, T., Ma, J., Ovchinnikov, V., Paci, E., Pastor, R. W., Post, C. B., Pu, J. Z., Schaefer, M., Tidor, B., Venable, R. M., Woodcock, H. L., Wu, X., Yang, W., York, D. M., Karplus, M., Brooks B.R., Brooks III C.L., Mackerell Jr. A.D., Nilsson L., Petrella R.J., Roux B., Won Y., Archontis G., Bartels C., Boresch S., Caflisch A., Caves L., Cui Q., Dinner A.R., Feig M., Fischer S., Gao J., Hodoscek M., Im W., Kuczera K., Lazaridis T., Ma J., Ovchinnikov V., Paci E., Pastor R.W., Post C.B., Pu J.Z., Schaefer M., Tidor B., Venable R.M., Woodcock H.L., Wu X., Yang W., York D.M., Karplus M., Archontis, Georgios Z. [0000-0002-7750-8641], and University of Zurich

Subjects
Models, Molecular, Potential energy functions, Molecular dynamic, Molecular model, chemical model, Energy functions, Molecular dynamics, Molecular mechanicals, Computational chemistry, Nucleic Acids, computer program, CHARMM program, Many-particle systems, Amines, Explicit solvents, Chemistry, biology, Small molecules, article, Potential energy, Lipids, peptide, Dynamics, Nucleic acids, Computational Mathematics, Molecular mechanic, symbols, Membrane models, Molecular simulations, Harvard, Biomolecular simulation, 2605 Computational Mathematics, Biophysical computation, Carbohydrates, Molecular modeling, 1600 General Chemistry, chemistry, Article, Computational science, symbols.namesake, Parallel architectures, lipid, Simulators, 10019 Department of Biochemistry, computer simulation, Computer Simulation, Molecular mechanics, Analysis techniques, Computational tools, Energy function, Computational Biology, Proteins, Quantum mechanical, General Chemistry, Mechanical force, quantum theory, nucleic acid, Implicit solvents, Models, Chemical, Path sampling method, carbohydrate, chemical structure, Quantum Theory, 570 Life sciences, Drude particle, protein, Peptides, Software
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. In addition, 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 paper provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM paper in 1983.

Published
2009
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