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The program can read or model build structures, energy minimize them by first\u2010 or second\u2010derivative techniques, perform a normal mode or molecular dynamics simulation, and analyze the structural, equilibrium, and dynamic properties determined in these calculations. The operations that CHARMM can perform are described, and some implementation details are given. A set of parameters for the empirical energy function and a sample run are included.\n                  <\/jats:p>","DOI":"10.1002\/jcc.540040211","type":"journal-article","created":{"date-parts":[[2004,12,28]],"date-time":"2004-12-28T13:40:30Z","timestamp":1104241230000},"page":"187-217","source":"Crossref","is-referenced-by-count":13678,"title":["<scp>CHARMM<\/scp>\n                    : A program for macromolecular energy, minimization, and dynamics calculations"],"prefix":"10.1002","volume":"4","author":[{"given":"Bernard R.","family":"Brooks","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert E.","family":"Bruccoleri","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Barry D.","family":"Olafson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David J.","family":"States","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S.","family":"Swaminathan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin","family":"Karplus","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2004,9,7]]},"reference":[{"key":"e_1_2_1_2_2","doi-asserted-by":"publisher","DOI":"10.1021\/ja01483a011"},{"key":"e_1_2_1_3_2","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(69)90421-5"},{"key":"e_1_2_1_4_2","doi-asserted-by":"publisher","DOI":"10.1021\/cr60270a003"},{"key":"e_1_2_1_5_2","doi-asserted-by":"publisher","DOI":"10.1021\/ja00805a012"},{"key":"e_1_2_1_6_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.pc.31.100180.000333"},{"key":"e_1_2_1_7_2","doi-asserted-by":"crossref","first-page":"628","DOI":"10.1016\/S0006-3495(80)84993-9","volume":"32","author":"Karplus M.","year":"1980","journal-title":"Biophys. 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