{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,4]],"date-time":"2024-08-04T07:17:17Z","timestamp":1722755837798},"reference-count":22,"publisher":"Wiley","issue":"3","license":[{"start":{"date-parts":[[2004,9,7]],"date-time":"2004-09-07T00:00:00Z","timestamp":1094515200000},"content-version":"vor","delay-in-days":4208,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J Comput Chem"],"published-print":{"date-parts":[[1993,3]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>A fully functional parallel version of the molecular dynamics (MD) module of AMBER3a has been implemented. Procedures parallelized include the calculation of the long\u2010range nonbonded Coulomb and Lennard\u2013Jones interactions, generation of the pairlist, intramolecular bond, angle, dihedral, 1\u20104 nonbonded interaction terms, coordinate restraints, and the SHAKE bond constraint algorithm. As far as we can determine, this is the first published description where a distributed\u2010memory MIMD parallel implementation of the SHAKE algorithm has been designed to treat not only <jats:italic>hydrogen<\/jats:italic>\u2010<jats:italic>containing bonds<\/jats:italic> but also <jats:italic>all heavy<\/jats:italic>\u2010<jats:italic>atom bonds<\/jats:italic>, and where \u201cshaken\u201d <jats:italic>crosslinks<\/jats:italic> are supported as well. We discuss the subtasking and partitioning of an MD time\u2010step, load balancing the nonbonded evaluations, describe in <jats:italic>algorithmic detail<\/jats:italic> how parallelization of SHAKE was accomplished, and present <jats:italic>speedup<\/jats:italic>, <jats:italic>efficiency, and benchmarking results<\/jats:italic> achieved when this hypercube adaptation of the MD module AMBER was applied to several variant molecular systems. Results are presented for speedup and efficiency obtained on the nCUBE machine, using up to 128 processors, as well as benchmarks for performance comparisons with the CRAY YMP and FPS522 vector machines. \u00a9 1993 John Wiley &amp; Sons, Inc.<\/jats:p>","DOI":"10.1002\/jcc.540140307","type":"journal-article","created":{"date-parts":[[2005,1,2]],"date-time":"2005-01-02T00:38:59Z","timestamp":1104626339000},"page":"312-329","source":"Crossref","is-referenced-by-count":26,"title":["AMBERCUBE MD, parallelization of Amber's molecular dynamics module for distributed\u2010memory hypercube computers"],"prefix":"10.1002","volume":"14","author":[{"given":"Stephen E.","family":"Debolt","sequence":"first","affiliation":[]},{"given":"Peter A.","family":"Kollman","sequence":"additional","affiliation":[]}],"member":"311","published-online":{"date-parts":[[2004,9,7]]},"reference":[{"key":"e_1_2_1_2_2","volume-title":"Solving Problems On Concurrent Processors. General Techniques And Regular Problems","author":"Fox G.C.","year":"1988"},{"key":"e_1_2_1_2_3","first-page":"57","volume-title":"Solving Problems On Concurrent Processors. General Techniques And Regular Problems"},{"key":"e_1_2_1_2_4","volume-title":"Solving Problems On Concurrent Processors. General Techniques And Regular Problems"},{"key":"e_1_2_1_2_5","first-page":"260","volume-title":"Solving Problems On Concurrent Processors. 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