@article{ CHARMM2009,
Author = {Brooks, B. R. and Brooks, III, C. L. and Mackerell, Jr., 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.},
Title = {{CHARMM: The Biomolecular Simulation Program}},
Journal = {{JOURNAL OF COMPUTATIONAL CHEMISTRY}},
Year = {{2009}},
Volume = {{30}},
Number = {{10, Sp. Iss. SI}},
Pages = {{1545-1614}},
Month = {{JUL 30}},
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. (C) 2009 Wiley Periodicals, Inc. J Comput Chem 30:
   1545-1614, 2009}},
Publisher = {{JOHN WILEY \& SONS INC}},
Address = {{111 RIVER ST, HOBOKEN, NJ 07030 USA}},
Type = {{Review}},
Language = {{English}},
Affiliation = {{Brooks, BR (Reprint Author), NHLBI, Lab Computat Biol, NIH, Bldg 10, Bethesda, MD 20892 USA.
   {[}Brooks, B. R.] NHLBI, Lab Computat Biol, NIH, Bethesda, MD 20892 USA.
   {[}Brooks, C. L., III] Univ Michigan, Dept Chem, Ann Arbor, MI 48109 USA.
   {[}Brooks, C. L., III] Univ Michigan, Dept Biophys, Ann Arbor, MI 48109 USA.
   {[}Mackerell, A. D., Jr.] Univ Maryland, Sch Pharm, Dept Pharmaceut Sci, Baltimore, MD 21201 USA.
   {[}Nilsson, L.] Karolinska Inst, Dept Biosci \& Nutr, SE-14157 Huddinge, Sweden.
   {[}Petrella, R. J.; Karplus, M.] Harvard Univ, Dept Chem \& Chem Biol, Cambridge, MA 02138 USA.
   {[}Petrella, R. J.] Harvard Univ, Sch Med, Dept Med, Boston, MA 02115 USA.
   {[}Roux, B.] Univ Chicago, Dept Biochem \& Mol Biol, Gordon Ctr Integrat Sci, Chicago, IL 60637 USA.
   {[}Won, Y.] Hanyang Univ, Dept Chem, Seoul 133792, South Korea.
   {[}Karplus, M.] Univ Strasbourg, ISIS, Lab Chim Biophys, F-67000 Strasbourg, France.}},
DOI = {{10.1002/jcc.21287}},
ISSN = {{0192-8651}},
Keywords = {{biomolecular simulation; CHARMM program; molecular mechanics; molecular
   dynamics; molecular modeling; biophysical computation; energy function}},
Keywords-Plus = {{MOLECULAR-DYNAMICS SIMULATIONS; FREE-ENERGY CALCULATIONS; IMPLICIT
   SOLVENT MODELS; EMPIRICAL FORCE-FIELD; MONTE-CARLO SIMULATIONS; BINDING
   FREE-ENERGIES; PARTICLE-MESH EWALD; INTERMOLECULAR POTENTIAL FUNCTION;
   CLASSICAL DRUDE OSCILLATOR; SIDE-CHAIN CONFORMATIONS}},
Subject-Category = {{Chemistry, Multidisciplinary}},
Author-Email = {{brbrooks@helix.nih.gov
   brookscl@umich.edu
   alex@outerbanks.umaryland.edu
   Lennart.Nilsson@ki.se
   petrella@fas.harvard.edu
   roux@uchicago.edu
   won@hanyang.ac.kr
   marci@tammy.harvard.edu}},
Funding-Acknowledgement = {{NIH {[}RR023920]; NSF ; DOE ; Accelrys ; CNRS ; NHLBI }},
Funding-Text = {{In a multiauthor article. there is a leuitimate concern that the people
   involved receive the credit that they deserve. In Peneral, this is not
   possible Without listing the contributions of each individual, as some
   journals are now requiring. For ail article of this length and
   complexity, however, an), attempt at such specific attribution of
   credit is impractical. All the authors contributed to the writing and
   rewriting of significant portions of the text. The corresponding
   authors. designated by asterisks, were also involved in planning the
   manuscript and overseeing sections in the early stages of the writing.
   In both groups (starred and unstarred), the listing is alphabetical.
   One author, R.J. Petrella, needs to be mentioned individually because,
   in addition to writing a significant portion of the article. he was
   instrumental in transforming a large number of separate write-ups into
   what is very nearly a unified whole.
   The authors thank the referees for their helpful comments and David A.
   Case for serving as the editor of the paper. A number of people, other
   than those in the author list, have read and commented on the
   manuscript. They include Kwangho Nam, Arjan van der Vaart, loan
   Andricioaei, and Tom Darden.
   In addition to all of the authors of the paper, many other scientists
   have participated significantly in the development of CHARMM through
   the years. See Table 3; this list is included with all distributions of
   the program (in ``charmm\_main.src{''}).
   Support for the development of CHARMM, per se, and for researchers
   concerned with CHARMM development, have come from many sources.
   including NSF, NIH, DOE, Accelrys, and CNRS. It is not possible to list
   all of the grants individually, but NIH grant RR023920 is acknowledged
   for its direct support of the ongoing CHARMM conversion project. Part
   of the research in the B.R. Brooks group was supported by the
   Intramural Research Program of the NIH, NHLBI.}},
Number-of-Cited-References = {{721}},
Times-Cited = {{7}},
Journal-ISO = {{J. Comput. Chem.}},
Doc-Delivery-Number = {{461LX}},
Unique-ID = {{ISI:000267269600001}},
}


@Article{ CHARMM1983,
   title = "CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations",
   author = "Brooks, B.R. and Bruccoleri, R.E. and Olafson, D.J. and States, D.J. and Swaminathan, S. and Karplus, M.",
   journal = "Journal of Computational Chemistry",
   pages = "187-217",
   volume = "4",
   year = "1983"
}

@InBook{ CHARMMFF,
   title = "CHARMM: The Energy Function and Its Parameterization with an Overview of the Program",
   series = "The Encyclopedia of Computational Chemistry",
   author = "MacKerel Jr., A.D. and Brooks III, C.L. and Nilsson, L. and Roux, B. and Won, Y. and Karplus, M.",
   editor = "P. v. R. Schleyer et al.",
   publisher = "John Wiley \& Sons: Chichester",
   pages = "271-277",
   volume = "1",
   year = "1998"
}