CHARMM: the biomolecular simulation program.

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TitleCHARMM: the biomolecular simulation program.
Publication TypeJournal Article
Year of Publication2009
AuthorsBrooks, BR, Brooks, CL, Mackerell, AD, Nilsson, L, Petrella, RJ, Roux, B, Won, Y, Archontis, G, Bartels, C, Boresch, S, Caflisch, A, Caves, L, Cui, Q, Dinner, AR, Feig, M, Fischer, S, Gao, J, Hodoscek, M, Im, W, Kuczera, K, Lazaridis, T, Ma, J, Ovchinnikov, V, Paci, E, Pastor, RW, Post, CB, Pu, JZ, Schaefer, M, Tidor, B, Venable, RM, Woodcock, HL, Wu, X, Yang, W, York, DM, Karplus, M
JournalJ Comput Chem
Volume30
Issue10
Pagination1545-614
Date Published2009 Jul 30
ISSN1096-987X
KeywordsCarbohydrates, Computational Biology, Computer Simulation, Lipids, Models, Chemical, Models, Molecular, Nucleic Acids, Peptides, Proteins, Quantum Theory, 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. 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.

DOI10.1002/jcc.21287
Alternate JournalJ Comput Chem
PubMed ID19444816
PubMed Central IDPMC2810661
Grant ListR01 GM030804-29 / GM / NIGMS NIH HHS / United States
R01 GM030804-32 / GM / NIGMS NIH HHS / United States
R01 RR023920 / RR / NCRR NIH HHS / United States
RR023920 / RR / NCRR NIH HHS / United States
Z01 HL001051-10 / / Intramural NIH HHS / United States
R01 GM030804-31 / GM / NIGMS NIH HHS / United States
R01 GM030804-34 / GM / NIGMS NIH HHS / United States
R01 GM082209 / GM / NIGMS NIH HHS / United States
R01 GM030804-38 / GM / NIGMS NIH HHS / United States
R01 GM030804-30 / GM / NIGMS NIH HHS / United States
R01 GM030804-35 / GM / NIGMS NIH HHS / United States
R01 RR023920-02 / RR / NCRR NIH HHS / United States
R01 GM030804-33 / GM / NIGMS NIH HHS / United States
F32 GM083422 / GM / NIGMS NIH HHS / United States
R01 GM065418 / GM / NIGMS NIH HHS / United States
R01 GM030804-39 / GM / NIGMS NIH HHS / United States
Z01 HL001052-10 / / Intramural NIH HHS / United States
R01 GM030804-37 / GM / NIGMS NIH HHS / United States
R01 GM030804-36 / GM / NIGMS NIH HHS / United States