{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T15:15:17Z","timestamp":1753888517257},"reference-count":23,"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":3294,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J Comput Chem"],"published-print":{"date-parts":[[1995,9]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>A parallel version of the popular molecular mechanics package AMBER suitable for execution on workstation clusters has been developed. Computer\u2010intensive portions of molecular dynamics or free\u2010energy perturbation computations, such as nonbonded pair list generation or calculation of nonbonded energies and forces, are distributed across a collection of Unix workstations linked by Ethernet or FDDI connections. This parallel implementation utilizes the message\u2010passing software PVM (Parallel Virtual Machine) from Oak Ridge National Laboratory to coordinate data exchange and processor synchronization. Test simulations performed for solvated peptide, protein, and lipid bilayer systems indicate that reasonable parallel efficiency (70\u201390%) and computational speedup (2\u20135 \u00d7 serial computer runtimes) can be achieved with small workstation clusters (typically six to eight machines) for typical biomolecular simulation problems. PVM\u2010AMBER is also easily and rapidly portable to different hardware platforms due to the availability of PVM for numerous computers. The current version of PVM\u2010AMBER has been tested successfully on Silicon Graphics, IBM RS6000, DEC ALPHA, and HP 735 workstation clusters and heterogeneous clusters of these machines, as well as on CRAY T3D and Kendall Square KSR2 parallel supercomputers. Thus, PVM\u2010AMBER provides a simple and cost\u2010effective mechanism for parallel molecular dynamics simulations on readily available hardware platforms. Factors that affect the efficiency of this approach are discussed. \u00a9 1995 by John Wiley &amp; Sons, Inc.<\/jats:p>","DOI":"10.1002\/jcc.540160907","type":"journal-article","created":{"date-parts":[[2005,1,2]],"date-time":"2005-01-02T01:10:01Z","timestamp":1104628201000},"page":"1131-1140","source":"Crossref","is-referenced-by-count":6,"title":["PVM\u2010AMBER: A parallel implementation of the AMBER molecular mechanics package for workstation clusters"],"prefix":"10.1002","volume":"16","author":[{"given":"Eric","family":"Swanson","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Terry P.","family":"Lybrand","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","unstructured":"D. A.Pearlman D. A.Case J. C.Caldwell G. L.Seibel U. C.Singh P.Weiner andP.Kollman Amber 4.0 University of California at San Francisco 1991"},{"key":"e_1_2_1_3_2","doi-asserted-by":"publisher","DOI":"10.1016\/0010-4809(92)90019-7"},{"key":"e_1_2_1_4_2","doi-asserted-by":"publisher","DOI":"10.1016\/0097-8485(90)80049-8"},{"key":"e_1_2_1_5_2","doi-asserted-by":"publisher","DOI":"10.1016\/0010-4655(90)90043-Z"},{"key":"e_1_2_1_6_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540121016"},{"key":"e_1_2_1_7_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540040211"},{"key":"e_1_2_1_8_2","series-title":"Proceedings Scalable High Performance Computing SHPCC\u201092","author":"Clark T. W.","year":"1992"},{"key":"e_1_2_1_9_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540130813"},{"key":"e_1_2_1_10_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540050311"},{"key":"e_1_2_1_11_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540120206"},{"key":"e_1_2_1_12_2","doi-asserted-by":"publisher","DOI":"10.1006\/jcph.1993.1094"},{"key":"e_1_2_1_13_2","doi-asserted-by":"publisher","DOI":"10.1016\/0167-8191(94)90021-3"},{"key":"e_1_2_1_13_3","unstructured":"The remainder of this issue describes specific message\u2010passing implementations."},{"key":"e_1_2_1_14_2","doi-asserted-by":"publisher","DOI":"10.1002\/cpe.4330040403"},{"key":"e_1_2_1_15_2","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1063\/1.4823162","volume":"7","author":"Donagarra J.","year":"1993","journal-title":"Comp. in Phys."},{"key":"e_1_2_1_15_3","unstructured":"PVM may be obtained by anonymous ftp from cs.utk.edu in directory pub\/xnetlib or via e\u2010mail server by sending the message \u201csend index from pym3\u201d tonetlib@ornl.gov."},{"key":"e_1_2_1_16_2","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1063\/1.4823163","volume":"7","author":"Duke D. W.","year":"1993","journal-title":"Comp. Phys."},{"key":"e_1_2_1_17_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(77)80200-3"},{"key":"e_1_2_1_18_2","unstructured":"C. C.Douglas T. G.Mattson andM. H.Schultz Parallel Programming Systems for Workstation Clusters Technical Report YALEU\/DCS\/TR\u2010975 Department of Computer Science Yale University 1993. (available fromcasper.na.cs.yale.edu in \/pub\/tr975.ps)"},{"key":"e_1_2_1_19_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540130414"},{"key":"e_1_2_1_20_2","series-title":"Proceedings Scalable High Performance Computing SHPCC\u201092","first-page":"113","author":"Sato H.","year":"1992"},{"key":"e_1_2_1_21_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540140307"},{"key":"e_1_2_1_22_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540150106"}],"container-title":["Journal of Computational Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.wiley.com\/onlinelibrary\/tdm\/v1\/articles\/10.1002%2Fjcc.540160907","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/jcc.540160907","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,10,27]],"date-time":"2023-10-27T01:10:36Z","timestamp":1698369036000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/jcc.540160907"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[1995,9]]},"references-count":23,"journal-issue":{"issue":"9","published-print":{"date-parts":[[1995,9]]}},"alternative-id":["10.1002\/jcc.540160907"],"URL":"https:\/\/doi.org\/10.1002\/jcc.540160907","archive":["Portico"],"relation":{},"ISSN":["0192-8651","1096-987X"],"issn-type":[{"value":"0192-8651","type":"print"},{"value":"1096-987X","type":"electronic"}],"subject":[],"published":{"date-parts":[[1995,9]]}}}