{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T15:27:55Z","timestamp":1753889275601},"reference-count":23,"publisher":"Wiley","issue":"11","license":[{"start":{"date-parts":[[2004,9,7]],"date-time":"2004-09-07T00:00:00Z","timestamp":1094515200000},"content-version":"vor","delay-in-days":3233,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J Comput Chem"],"published-print":{"date-parts":[[1995,11]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>We have implemented a portable parallel version of the macromolecular modeling package AMBER4. The message passing paradigm was used. All message passing constructs are compliant with the Message Passing Interface (MPI) standard. The molecular dynamics\/minimization module MINMD and the free\u2010energy perturbation module Gibbs have been implemented in parallel on a number of machines, including a Cray T3D, an IBM SP1\/SP2, and a collection of networked workstations. In addition, the code has been tested with an MPI implementation from Argonne National Laboratories\/Mississippi State University which runs on many parallel machines. The goal of this work is to decrease the amount of time required to perform molecular dynamics simulations. Performance results for a lipid bilayer molecular dynamics simulation on a Cray T3D, an IBM SP1\/SP2, and a Cray C90 are compared. \u00a9 1995 John Wiley &amp; Sons, Inc.<\/jats:p>","DOI":"10.1002\/jcc.540161110","type":"journal-article","created":{"date-parts":[[2005,1,2]],"date-time":"2005-01-02T01:07:15Z","timestamp":1104628035000},"page":"1420-1427","source":"Crossref","is-referenced-by-count":24,"title":["A highly portable parallel implementation of AMBER4 using the message passing interface standard"],"prefix":"10.1002","volume":"16","author":[{"given":"James J.","family":"Vincent","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"suffix":"Jr.","given":"Kenneth M.","family":"Merz","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2004,9,7]]},"reference":[{"key":"e_1_2_1_2_2","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4471-1842-8","volume-title":"Past, Present, Parallel: A Survey of Available Parallel Computer Systems","author":"Trew A.","year":"1991"},{"key":"e_1_2_1_3_2","doi-asserted-by":"publisher","DOI":"10.1007\/BF01113948"},{"key":"e_1_2_1_4_2","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1002\/cpe.4330040503","volume":"4","author":"Hauser J.","year":"1992","journal-title":"Concurr.: Practice Exper."},{"key":"e_1_2_1_5_2","first-page":"377","volume":"8","author":"Jones R.","year":"1992","journal-title":"Comp. Applic. Biosci."},{"key":"e_1_2_1_6_2","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1017\/S0022112093002332","volume":"254","author":"Simon H. D.","year":"1993","journal-title":"J. Fluid Mech."},{"key":"e_1_2_1_7_2","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1007\/BF01113265","volume":"84","author":"Harrison R.","year":"1993","journal-title":"Theoret. Chim. Acta"},{"key":"e_1_2_1_8_2","doi-asserted-by":"publisher","DOI":"10.1002\/qua.560460104"},{"key":"e_1_2_1_9_2","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1063\/1.168448","volume":"6","author":"Hoover W. G.","year":"1992","journal-title":"Comput. Phys."},{"key":"e_1_2_1_10_2","doi-asserted-by":"publisher","DOI":"10.1016\/0167-8191(92)90091-K"},{"key":"e_1_2_1_11_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540130414"},{"key":"e_1_2_1_12_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540140202"},{"key":"e_1_2_1_13_2","doi-asserted-by":"publisher","DOI":"10.1016\/0010-4655(91)90097-5"},{"key":"e_1_2_1_14_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540151006"},{"key":"e_1_2_1_15_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540121016"},{"key":"e_1_2_1_16_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540140307"},{"key":"e_1_2_1_17_2","unstructured":"Message Passing Interface Forum MPI Document for a Standard Message Passing Interface University of Tennessee 1994."},{"key":"e_1_2_1_18_2","doi-asserted-by":"publisher","DOI":"10.1016\/0010-4655(94)90229-1"},{"key":"e_1_2_1_19_2","doi-asserted-by":"publisher","DOI":"10.1021\/ja00315a051"},{"key":"e_1_2_1_20_2","doi-asserted-by":"publisher","DOI":"10.1016\/0167-8191(93)90027-I"},{"key":"e_1_2_1_21_2","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1016\/0167-8191(94)90113-9","volume":"20","author":"Calinescu R.","year":"1994","journal-title":"Parall. Comput."},{"key":"e_1_2_1_22_2","doi-asserted-by":"publisher","DOI":"10.1006\/jpdc.1994.1070"},{"key":"e_1_2_1_23_2","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1016\/0010-4655(94)90183-X","volume":"79","author":"Altevogt P.","year":"1994","journal-title":"Comp. Phys. Commun."},{"key":"e_1_2_1_24_2","volume-title":"SHMEM Users Guide","author":"Barriuso R.","year":"1994"}],"container-title":["Journal of Computational Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.wiley.com\/onlinelibrary\/tdm\/v1\/articles\/10.1002%2Fjcc.540161110","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/jcc.540161110","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,10,25]],"date-time":"2023-10-25T20:27:47Z","timestamp":1698265667000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/jcc.540161110"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[1995,11]]},"references-count":23,"journal-issue":{"issue":"11","published-print":{"date-parts":[[1995,11]]}},"alternative-id":["10.1002\/jcc.540161110"],"URL":"https:\/\/doi.org\/10.1002\/jcc.540161110","archive":["Portico"],"relation":{},"ISSN":["0192-8651","1096-987X"],"issn-type":[{"value":"0192-8651","type":"print"},{"value":"1096-987X","type":"electronic"}],"subject":[],"published":{"date-parts":[[1995,11]]}}}