CHARMM: The biomolecular simulation program Export

@article{citeulike:4528480, 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. {\copyright} 2009 Wiley Periodicals, Inc.J Comput Chem, 2009.}, address = {Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892; Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109; Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109; Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201; Department of Biosciences and Nutrition, Karolinska Institutet, SE-141 57, Huddinge, Sweden; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138; Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115; Department of Biochemistry and Molecular Biology, University of Chicago, Gordon Center for Integrative Science, Chicago, Illinois 60637; Department of Chemistry, Hanyang University, Seoul 133-792, Korea; Laboratoire de Chimie Biophysique, ISIS, Universit\'{e} de Strasbourg, 67000 Strasbourg, France}, author = {Brooks, B. R. and Brooks, C. L. and Mackerell, A. D. and Nilsson, L. and Petrella, R. J. and Roux, B. and Won, Y. and Archontis, G. and Bartels, C. and Boresch, S. and Caflisch, A. and Caves, L. and Cui, Q. and Dinner, A. R. and Feig, M. and Fischer, S. and Gao, J. and Hodoscek, M. and Im, W. and Kuczera, K. and Lazaridis, T. and Ma, J. and Ovchinnikov, V. and Paci, E. and Pastor, R. W. and Post, C. B. and Pu, J. Z. and Schaefer, M. and Tidor, B. and Venable, R. M. and Woodcock, H. L. and Wu, X. and Yang, W. and York, D. M. and Karplus, M.}, citeulike-article-id = {4528480}, citeulike-linkout-0 = {http://dx.doi.org/10.1002/jcc.21287}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19444816}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19444816}, citeulike-linkout-3 = {http://www3.interscience.wiley.com/cgi-bin/abstract/122385019/ABSTRACT}, day = {30}, doi = {10.1002/jcc.21287}, issn = {1096-987X}, journal = {Journal of Computational Chemistry}, keywords = {molecular\_dynamics, molecular\_simulation}, month = {July}, number = {10}, pages = {1545--1614}, posted-at = {2009-05-19 12:00:47}, priority = {2}, title = {CHARMM: The biomolecular simulation program}, url = {http://dx.doi.org/10.1002/jcc.21287}, volume = {30}, year = {2009} }

TY - JOUR ID - citeulike:4528480 L3 - citeulike-article-id:4528480 N2 - 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. IS - 10 JF - Journal of Computational Chemistry SN - 1096-987X AD - Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892; Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109; Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109; Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201; Department of Biosciences and Nutrition, Karolinska Institutet, SE-141 57, Huddinge, Sweden; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138; Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115; Department of Biochemistry and Molecular Biology, University of Chicago, Gordon Center for Integrative Science, Chicago, Illinois 60637; Department of Chemistry, Hanyang University, Seoul 133-792, Korea; Laboratoire de Chimie Biophysique, ISIS, Université de Strasbourg, 67000 Strasbourg, France EP - 1614 TI - CHARMM: The biomolecular simulation program VL - 30 SP - 1545 KW - molecular_dynamics KW - molecular_simulation AU - Brooks, BR AU - Brooks, CL AU - Mackerell, AD AU - Nilsson, L AU - Petrella, RJ AU - Roux, B AU - Won, Y AU - Archontis, G AU - Bartels, C AU - Boresch, S AU - Caflisch, A AU - Caves, L AU - Cui, Q AU - Dinner, AR AU - Feig, M AU - Fischer, S AU - Gao, J AU - Hodoscek, M AU - Im, W AU - Kuczera, K AU - Lazaridis, T AU - Ma, J AU - Ovchinnikov, V AU - Paci, E AU - Pastor, RW AU - Post, CB AU - Pu, JZ AU - Schaefer, M AU - Tidor, B AU - Venable, RM AU - Woodcock, HL AU - Wu, X AU - Yang, W AU - York, DM AU - Karplus, M PY - 2009/07/30/ UR - http://dx.doi.org/10.1002/jcc.21287 ER -