{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,24]],"date-time":"2025-10-24T12:50:22Z","timestamp":1761310222219},"reference-count":28,"publisher":"Wiley","issue":"9","license":[{"start":{"date-parts":[[2004,9,7]],"date-time":"2004-09-07T00:00:00Z","timestamp":1094515200000},"content-version":"vor","delay-in-days":3659,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J Comput Chem"],"published-print":{"date-parts":[[1994,9]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>We present a novel algorithm of constrained, overdamped dynamics to study the long\u2010time properties of peptides, proteins, and related molecules. The constraints are applied to an all\u2010atom model of the molecule by projecting out all components of the nonbonding interactions which tend to alter fixed bond lengths and angles. Because the overdamped dynamical equations are first order in time, the constraints are satisfied by inversion of a banded matrix at each timestep, which is computationally efficient. Thermal effects are included through a Langevin noise term in the equation of motion. Because high\u2010frequency components of the motion have been eliminated, the timestep of the algorithm is determined by the nonbonding forces, which are two to three orders of magnitude weaker than the bonding forces. Using polyalanine as a test example, we demonstrate that trajectories simulating a microsecond of motion can be run about 10<jats:sup>3<\/jats:sup> times faster than an equivalent molecular dynamics simulation. \u00a9 1994 by John Wiley &amp; Sons, Inc.<\/jats:p>","DOI":"10.1002\/jcc.540150908","type":"journal-article","created":{"date-parts":[[2005,1,2]],"date-time":"2005-01-02T01:06:14Z","timestamp":1104627974000},"page":"997-1012","source":"Crossref","is-referenced-by-count":34,"title":["Long\u2010time overdamped Langevin dynamics of molecular chains"],"prefix":"10.1002","volume":"15","author":[{"given":"Niels","family":"Gr\u00f8nbech\u2010jensen","sequence":"first","affiliation":[]},{"given":"Sebastian","family":"Doniach","sequence":"additional","affiliation":[]}],"member":"311","published-online":{"date-parts":[[2004,9,7]]},"reference":[{"key":"e_1_2_1_2_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.459452"},{"key":"e_1_2_1_3_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(65)80171-1"},{"key":"e_1_2_1_4_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.84.22.7933"},{"issue":"12","key":"e_1_2_1_5_2","doi-asserted-by":"crossref","first-page":"7344","DOI":"10.1063\/1.451373","volume":"85","author":"Lamm G.","year":"1986","journal-title":"J. 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