{"id":"https://openalex.org/W2079195579","doi":"https://doi.org/10.1002/jcc.540160907","title":"PVM\u2010AMBER: A parallel implementation of the AMBER molecular mechanics package for workstation clusters","display_name":"PVM\u2010AMBER: A parallel implementation of the AMBER molecular mechanics package for workstation clusters","publication_year":1995,"publication_date":"1995-09-01","ids":{"openalex":"https://openalex.org/W2079195579","doi":"https://doi.org/10.1002/jcc.540160907","mag":"2079195579"},"language":"en","primary_location":{"id":"doi:10.1002/jcc.540160907","is_oa":false,"landing_page_url":"https://doi.org/10.1002/jcc.540160907","pdf_url":null,"source":{"id":"https://openalex.org/S21117631","display_name":"Journal of Computational Chemistry","issn_l":"0192-8651","issn":["0192-8651","1096-987X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Chemistry","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5088606555","display_name":"Eric S. Swanson","orcid":"https://orcid.org/0000-0001-7394-9215"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210142217","display_name":"Washington Center","ror":"https://ror.org/03msb7010","country_code":"US","type":"other","lineage":["https://openalex.org/I4210142217"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eric Swanson","raw_affiliation_strings":["University of Washington, Center for Bioengineering, Molecular Bioengineering Program, Box 351750, Seattle, Washington 98195-1750","University of Washington, Center for Bioengineering, Molecular Bioengineering Program, Box 351750, Seattle, Washington 98195\u20101750"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Washington, Center for Bioengineering, Molecular Bioengineering Program, Box 351750, Seattle, Washington 98195-1750","institution_ids":["https://openalex.org/I201448701","https://openalex.org/I4210142217"]},{"raw_affiliation_string":"University of Washington, Center for Bioengineering, Molecular Bioengineering Program, Box 351750, Seattle, Washington 98195\u20101750","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5078740022","display_name":"Terry P. Lybrand","orcid":"https://orcid.org/0000-0002-2248-104X"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210142217","display_name":"Washington Center","ror":"https://ror.org/03msb7010","country_code":"US","type":"other","lineage":["https://openalex.org/I4210142217"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Terry P. Lybrand","raw_affiliation_strings":["University of Washington, Center for Bioengineering, Molecular Bioengineering Program, Box 351750, Seattle, Washington 98195-1750","University of Washington, Center for Bioengineering, Molecular Bioengineering Program, Box 351750, Seattle, Washington 98195\u20101750"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Washington, Center for Bioengineering, Molecular Bioengineering Program, Box 351750, Seattle, Washington 98195-1750","institution_ids":["https://openalex.org/I201448701","https://openalex.org/I4210142217"]},{"raw_affiliation_string":"University of Washington, Center for Bioengineering, Molecular Bioengineering Program, Box 351750, Seattle, Washington 98195\u20101750","institution_ids":["https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5078740022"],"corresponding_institution_ids":["https://openalex.org/I201448701","https://openalex.org/I4210142217"],"apc_list":{"value":4520,"currency":"USD","value_usd":4520},"apc_paid":null,"fwci":0.3864,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.57547765,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"16","issue":"9","first_page":"1131","last_page":"1140"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9965000152587891,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9965000152587891,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.989300012588501,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11247","display_name":"Plant nutrient uptake and metabolism","score":0.9828000068664551,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.821862518787384},{"id":"https://openalex.org/keywords/workstation","display_name":"Workstation","score":0.7880312204360962},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.6982938647270203},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.5815407633781433},{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.4954301118850708},{"id":"https://openalex.org/keywords/virtual-machine","display_name":"Virtual machine","score":0.47699812054634094},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.4769241511821747},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.442203164100647},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.4158717691898346},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.249930739402771},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.10477840900421143}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.821862518787384},{"id":"https://openalex.org/C67953723","wikidata":"https://www.wikidata.org/wiki/Q192525","display_name":"Workstation","level":2,"score":0.7880312204360962},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.6982938647270203},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.5815407633781433},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.4954301118850708},{"id":"https://openalex.org/C25344961","wikidata":"https://www.wikidata.org/wiki/Q192726","display_name":"Virtual machine","level":2,"score":0.47699812054634094},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.4769241511821747},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.442203164100647},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.4158717691898346},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.249930739402771},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.10477840900421143}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1002/jcc.540160907","is_oa":false,"landing_page_url":"https://doi.org/10.1002/jcc.540160907","pdf_url":null,"source":{"id":"https://openalex.org/S21117631","display_name":"Journal of Computational Chemistry","issn_l":"0192-8651","issn":["0192-8651","1096-987X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Chemistry","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","score":0.7400000095367432,"display_name":"Affordable and clean energy"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320310094","display_name":"University of Washington","ror":"https://ror.org/00cvxb145"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":18,"referenced_works":["https://openalex.org/W1966041739","https://openalex.org/W1972783998","https://openalex.org/W1973671260","https://openalex.org/W1991117456","https://openalex.org/W2001182505","https://openalex.org/W2006774019","https://openalex.org/W2010542899","https://openalex.org/W2014439731","https://openalex.org/W2014521953","https://openalex.org/W2014570683","https://openalex.org/W2026181001","https://openalex.org/W2041669624","https://openalex.org/W2062256089","https://openalex.org/W2090702565","https://openalex.org/W2149489299","https://openalex.org/W2150750358","https://openalex.org/W2161211209","https://openalex.org/W2162166182"],"related_works":["https://openalex.org/W2058965144","https://openalex.org/W2164382479","https://openalex.org/W98480971","https://openalex.org/W2150291671","https://openalex.org/W2027972911","https://openalex.org/W2146343568","https://openalex.org/W2152751187","https://openalex.org/W2134581225","https://openalex.org/W1970565298","https://openalex.org/W1605425324"],"abstract_inverted_index":{"Abstract":[0],"A":[1],"parallel":[2,57,93,178,189],"version":[3,143],"of":[4,22,37,47,136,144,165,203],"the":[5,60,134,201],"popular":[6],"molecular":[7,23,190],"mechanics":[8],"package":[9],"AMBER":[10],"suitable":[11],"for":[12,82,116,138,188],"execution":[13],"on":[14,150,171,193],"workstation":[15,109,160],"clusters":[16,110,161,164],"has":[17,146],"been":[18,147],"developed.":[19],"Computer\u2010intensive":[20],"portions":[21],"dynamics":[24,191],"or":[25,35,53],"free\u2010energy":[26],"perturbation":[27],"computations,":[28],"such":[29],"as":[30,168,170],"nonbonded":[31,38],"pair":[32],"list":[33],"generation":[34],"calculation":[36],"energies":[39],"and":[40,76,86,96,125,157,162,174,185],"forces,":[41],"are":[42,206],"distributed":[43],"across":[44],"a":[45,183],"collection":[46],"Unix":[48],"workstations":[49],"linked":[50],"by":[51,210],"Ethernet":[52],"FDDI":[54],"connections.":[55],"This":[56],"implementation":[58],"utilizes":[59],"message\u2010passing":[61],"software":[62],"PVM":[63,137],"(Parallel":[64],"Virtual":[65],"Machine)":[66],"from":[67],"Oak":[68],"Ridge":[69],"National":[70],"Laboratory":[71],"to":[72,113,128,133],"coordinate":[73],"data":[74],"exchange":[75],"processor":[77],"synchronization.":[78],"Test":[79],"simulations":[80,192],"performed":[81],"solvated":[83],"peptide,":[84],"protein,":[85],"lipid":[87],"bilayer":[88],"systems":[89],"indicate":[90],"that":[91,199],"reasonable":[92],"efficiency":[94,202],"(70\u201390%)":[95],"computational":[97],"speedup":[98],"(2\u20135":[99],"\u00d7":[100],"serial":[101],"computer":[102],"runtimes)":[103],"can":[104],"be":[105],"achieved":[106],"with":[107],"small":[108],"(typically":[111],"six":[112],"eight":[114],"machines)":[115],"typical":[117],"biomolecular":[118],"simulation":[119],"problems.":[120],"PVM\u2010AMBER":[121,145,181],"is":[122],"also":[123],"easily":[124],"rapidly":[126],"portable":[127],"different":[129],"hardware":[130,196],"platforms":[131],"due":[132],"availability":[135],"numerous":[139],"computers.":[140],"The":[141],"current":[142],"tested":[148],"successfully":[149],"Silicon":[151],"Graphics,":[152],"IBM":[153],"RS6000,":[154],"DEC":[155],"ALPHA,":[156],"HP":[158],"735":[159],"heterogeneous":[163],"these":[166],"machines,":[167],"well":[169],"CRAY":[172],"T3D":[173],"Kendall":[175],"Square":[176],"KSR2":[177],"supercomputers.":[179],"Thus,":[180],"provides":[182],"simple":[184],"cost\u2010effective":[186],"mechanism":[187],"readily":[194],"available":[195],"platforms.":[197],"Factors":[198],"affect":[200],"this":[204],"approach":[205],"discussed.":[207],"\u00a9":[208],"1995":[209],"John":[211],"Wiley":[212],"&":[213],"Sons,":[214],"Inc.":[215]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}