{"id":"https://openalex.org/W2156871002","doi":"https://doi.org/10.1177/109434209601000401","title":"NAMD: a Parallel, Object-Oriented Molecular Dynamics Program","display_name":"NAMD: a Parallel, Object-Oriented Molecular Dynamics Program","publication_year":1996,"publication_date":"1996-12-01","ids":{"openalex":"https://openalex.org/W2156871002","doi":"https://doi.org/10.1177/109434209601000401","mag":"2156871002"},"language":"en","primary_location":{"id":"doi:10.1177/109434209601000401","is_oa":false,"landing_page_url":"https://doi.org/10.1177/109434209601000401","pdf_url":null,"source":{"id":"https://openalex.org/S4210228336","display_name":"The International Journal of Supercomputer Applications and High Performance Computing","issn_l":"1078-3482","issn":["1078-3482"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The International Journal of Supercomputer Applications and High Performance Computing","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/A5080169992","display_name":"Mark T. Nelson","orcid":"https://orcid.org/0000-0001-9023-051X"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]},{"id":"https://openalex.org/I183874917","display_name":"Urbana University","ror":"https://ror.org/04kp3hw27","country_code":"US","type":"education","lineage":["https://openalex.org/I183874917"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mark T. Nelson","raw_affiliation_strings":["THEORETICAL BIOPHYSICS GROUP UNIVERSITY OF ILLINOIS\rAND BECKMAN INSTITUTE URBANA, IL 61801","THEORETICAL BIOPHYSICS GROUP UNIVERSITY OF ILLINOIS AND BECKMAN INSTITUTE URBANA, IL 61801"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"THEORETICAL BIOPHYSICS GROUP UNIVERSITY OF ILLINOIS\rAND BECKMAN INSTITUTE URBANA, IL 61801","institution_ids":["https://openalex.org/I183874917"]},{"raw_affiliation_string":"THEORETICAL BIOPHYSICS GROUP UNIVERSITY OF ILLINOIS AND BECKMAN INSTITUTE URBANA, IL 61801","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006129599","display_name":"William Humphrey","orcid":"https://orcid.org/0000-0003-4359-4913"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]},{"id":"https://openalex.org/I183874917","display_name":"Urbana University","ror":"https://ror.org/04kp3hw27","country_code":"US","type":"education","lineage":["https://openalex.org/I183874917"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"William Humphrey","raw_affiliation_strings":["THEORETICAL BIOPHYSICS GROUP UNIVERSITY OF ILLINOIS\rAND BECKMAN INSTITUTE URBANA, IL 61801","THEORETICAL BIOPHYSICS GROUP UNIVERSITY OF ILLINOIS AND BECKMAN INSTITUTE URBANA, IL 61801"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"THEORETICAL BIOPHYSICS GROUP UNIVERSITY OF ILLINOIS\rAND BECKMAN INSTITUTE URBANA, IL 61801","institution_ids":["https://openalex.org/I183874917"]},{"raw_affiliation_string":"THEORETICAL BIOPHYSICS GROUP UNIVERSITY OF ILLINOIS AND BECKMAN INSTITUTE URBANA, IL 61801","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036278069","display_name":"Attila G\u00fcrsoy","orcid":"https://orcid.org/0000-0002-2297-2113"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]},{"id":"https://openalex.org/I183874917","display_name":"Urbana University","ror":"https://ror.org/04kp3hw27","country_code":"US","type":"education","lineage":["https://openalex.org/I183874917"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Attila Gursoy","raw_affiliation_strings":["THEORETICAL BIOPHYSICS GROUP UNIVERSITY OF ILLINOIS\rAND BECKMAN INSTITUTE URBANA, IL 61801","THEORETICAL BIOPHYSICS GROUP UNIVERSITY OF ILLINOIS AND BECKMAN INSTITUTE URBANA, IL 61801"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"THEORETICAL BIOPHYSICS GROUP UNIVERSITY OF ILLINOIS\rAND BECKMAN INSTITUTE URBANA, IL 61801","institution_ids":["https://openalex.org/I183874917"]},{"raw_affiliation_string":"THEORETICAL BIOPHYSICS GROUP UNIVERSITY OF ILLINOIS AND BECKMAN INSTITUTE URBANA, IL 61801","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015421859","display_name":"Andrew Dalke","orcid":"https://orcid.org/0000-0001-8933-8830"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]},{"id":"https://openalex.org/I183874917","display_name":"Urbana University","ror":"https://ror.org/04kp3hw27","country_code":"US","type":"education","lineage":["https://openalex.org/I183874917"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andrew Dalke","raw_affiliation_strings":["THEORETICAL BIOPHYSICS GROUP UNIVERSITY OF ILLINOIS\rAND BECKMAN INSTITUTE URBANA, IL 61801","THEORETICAL BIOPHYSICS GROUP UNIVERSITY OF ILLINOIS AND BECKMAN INSTITUTE URBANA, IL 61801"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"THEORETICAL BIOPHYSICS GROUP UNIVERSITY OF ILLINOIS\rAND BECKMAN INSTITUTE URBANA, IL 61801","institution_ids":["https://openalex.org/I183874917"]},{"raw_affiliation_string":"THEORETICAL BIOPHYSICS GROUP UNIVERSITY OF ILLINOIS AND BECKMAN INSTITUTE URBANA, IL 61801","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051465480","display_name":"Laxmikant V. Kal\u00e9","orcid":"https://orcid.org/0000-0001-9673-8445"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]},{"id":"https://openalex.org/I183874917","display_name":"Urbana University","ror":"https://ror.org/04kp3hw27","country_code":"US","type":"education","lineage":["https://openalex.org/I183874917"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Laxmikant V. Kal\u00e9","raw_affiliation_strings":["THEORETICAL BIOPHYSICS GROUP UNIVERSITY OF ILLINOIS\rAND BECKMAN INSTITUTE URBANA, IL 61801","THEORETICAL BIOPHYSICS GROUP UNIVERSITY OF ILLINOIS AND BECKMAN INSTITUTE URBANA, IL 61801"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"THEORETICAL BIOPHYSICS GROUP UNIVERSITY OF ILLINOIS\rAND BECKMAN INSTITUTE URBANA, IL 61801","institution_ids":["https://openalex.org/I183874917"]},{"raw_affiliation_string":"THEORETICAL BIOPHYSICS GROUP UNIVERSITY OF ILLINOIS AND BECKMAN INSTITUTE URBANA, IL 61801","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049797937","display_name":"Robert D. Skeel","orcid":"https://orcid.org/0000-0002-4807-8988"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]},{"id":"https://openalex.org/I183874917","display_name":"Urbana University","ror":"https://ror.org/04kp3hw27","country_code":"US","type":"education","lineage":["https://openalex.org/I183874917"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert D. Skeel","raw_affiliation_strings":["THEORETICAL BIOPHYSICS GROUP UNIVERSITY OF ILLINOIS\rAND BECKMAN INSTITUTE URBANA, IL 61801","THEORETICAL BIOPHYSICS GROUP UNIVERSITY OF ILLINOIS AND BECKMAN INSTITUTE URBANA, IL 61801"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"THEORETICAL BIOPHYSICS GROUP UNIVERSITY OF ILLINOIS\rAND BECKMAN INSTITUTE URBANA, IL 61801","institution_ids":["https://openalex.org/I183874917"]},{"raw_affiliation_string":"THEORETICAL BIOPHYSICS GROUP UNIVERSITY OF ILLINOIS AND BECKMAN INSTITUTE URBANA, IL 61801","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5029996336","display_name":"Klaus Schulten","orcid":"https://orcid.org/0000-0001-7192-9632"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]},{"id":"https://openalex.org/I183874917","display_name":"Urbana University","ror":"https://ror.org/04kp3hw27","country_code":"US","type":"education","lineage":["https://openalex.org/I183874917"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Klaus Schulten","raw_affiliation_strings":["THEORETICAL BIOPHYSICS GROUP UNIVERSITY OF ILLINOIS\rAND BECKMAN INSTITUTE URBANA, IL 61801","THEORETICAL BIOPHYSICS GROUP UNIVERSITY OF ILLINOIS AND BECKMAN INSTITUTE URBANA, IL 61801"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"THEORETICAL BIOPHYSICS GROUP UNIVERSITY OF ILLINOIS\rAND BECKMAN INSTITUTE URBANA, IL 61801","institution_ids":["https://openalex.org/I183874917"]},{"raw_affiliation_string":"THEORETICAL BIOPHYSICS GROUP UNIVERSITY OF ILLINOIS AND BECKMAN INSTITUTE URBANA, IL 61801","institution_ids":["https://openalex.org/I157725225"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":4.5177,"has_fulltext":false,"cited_by_count":569,"citation_normalized_percentile":{"value":0.95661922,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"10","issue":"4","first_page":"251","last_page":"268"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9991000294685364,"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":0.9991000294685364,"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":0.9966999888420105,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9891999959945679,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7790123224258423},{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.5763747692108154},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.5352640151977539},{"id":"https://openalex.org/keywords/object","display_name":"Object (grammar)","score":0.5111845135688782},{"id":"https://openalex.org/keywords/dynamics","display_name":"Dynamics (music)","score":0.41979917883872986},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.4075908362865448},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.2514825165271759},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.18907397985458374},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.06275597214698792}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7790123224258423},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.5763747692108154},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.5352640151977539},{"id":"https://openalex.org/C2781238097","wikidata":"https://www.wikidata.org/wiki/Q175026","display_name":"Object (grammar)","level":2,"score":0.5111845135688782},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.41979917883872986},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.4075908362865448},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.2514825165271759},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.18907397985458374},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.06275597214698792},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1177/109434209601000401","is_oa":false,"landing_page_url":"https://doi.org/10.1177/109434209601000401","pdf_url":null,"source":{"id":"https://openalex.org/S4210228336","display_name":"The International Journal of Supercomputer Applications and High Performance Computing","issn_l":"1078-3482","issn":["1078-3482"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The International Journal of Supercomputer Applications and High Performance Computing","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.5099999904632568,"id":"https://metadata.un.org/sdg/6","display_name":"Clean water and sanitation"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320309622","display_name":"Harvard University","ror":"https://ror.org/03vek6s52"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332222","display_name":"University of Illinois at Urbana-Champaign","ror":"https://ror.org/047426m28"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":39,"referenced_works":["https://openalex.org/W8607506","https://openalex.org/W133208775","https://openalex.org/W309792073","https://openalex.org/W317880409","https://openalex.org/W656827624","https://openalex.org/W1964999566","https://openalex.org/W1969505913","https://openalex.org/W1970747580","https://openalex.org/W1972300242","https://openalex.org/W1982252166","https://openalex.org/W1982338804","https://openalex.org/W2010590930","https://openalex.org/W2026771549","https://openalex.org/W2033709017","https://openalex.org/W2041902442","https://openalex.org/W2051519450","https://openalex.org/W2063060974","https://openalex.org/W2065510140","https://openalex.org/W2068306188","https://openalex.org/W2069953906","https://openalex.org/W2071740908","https://openalex.org/W2071950147","https://openalex.org/W2079577430","https://openalex.org/W2083206954","https://openalex.org/W2088624299","https://openalex.org/W2096825605","https://openalex.org/W2111516947","https://openalex.org/W2132185105","https://openalex.org/W2132521630","https://openalex.org/W2138199172","https://openalex.org/W2145812623","https://openalex.org/W2152509830","https://openalex.org/W2155066383","https://openalex.org/W2162166182","https://openalex.org/W2482997221","https://openalex.org/W3016119576","https://openalex.org/W4234347480","https://openalex.org/W4299790875","https://openalex.org/W4301350434"],"related_works":["https://openalex.org/W2023156907","https://openalex.org/W3094899115","https://openalex.org/W1968806281","https://openalex.org/W3095515585","https://openalex.org/W4315498887","https://openalex.org/W2737719445","https://openalex.org/W4239098401","https://openalex.org/W4378377190","https://openalex.org/W4401585471","https://openalex.org/W1773535258"],"abstract_inverted_index":{"NAMD":[0,34,55,73,104],"is":[1,46],"a":[2,41,78,82,98,106],"molecular":[3,83],"dynamics":[4],"program":[5,85],"designed":[6],"for":[7,64,94],"high":[8],"performance":[9,115],"simulations":[10],"of":[11,28,103,109,116],"large":[12],"biomolecular":[13],"systems":[14],"on":[15],"parallel":[16],"computers.":[17],"An":[18],"object-oriented":[19],"design":[20],"imple":[21],"mented":[22],"using":[23],"C++":[24],"facilitates":[25],"the":[26,32,57,114],"incorporation":[27],"new":[29],"algorithms":[30],"into":[31],"program.":[33],"uses":[35],"spatial":[36],"decom":[37],"position":[38],"coupled":[39],"with":[40],"multithreaded,":[42],"message-driven":[43],"design,":[44],"which":[45],"shown":[47],"to":[48,51,81,88,105],"scale":[49],"efficiently":[50],"multiple":[52],"processors.":[53],"Also,":[54],"incorporates":[56],"distributed":[58],"par":[59],"allel":[60],"multipole":[61],"tree":[62],"algorithm":[63],"full":[65],"electrostatic":[66],"force":[67],"evaluation":[68],"in":[69,86],"O(":[70],"N)":[71],"time.":[72],"can":[74],"be":[75],"connected":[76],"via":[77],"communication":[79],"system":[80,108],"graphics":[84],"order":[87],"provide":[89],"an":[90],"interactive":[91],"modeling":[92],"tool":[93],"viewing":[95],"and":[96],"modifying":[97],"running":[99],"simulation.":[100],"The":[101],"application":[102],"protein-water":[107],"32,867":[110],"atoms":[111],"illus":[112],"trates":[113],"NAMD.":[117]},"counts_by_year":[{"year":2026,"cited_by_count":8},{"year":2025,"cited_by_count":20},{"year":2024,"cited_by_count":32},{"year":2023,"cited_by_count":33},{"year":2022,"cited_by_count":34},{"year":2021,"cited_by_count":38},{"year":2020,"cited_by_count":30},{"year":2019,"cited_by_count":24},{"year":2018,"cited_by_count":17},{"year":2017,"cited_by_count":22},{"year":2016,"cited_by_count":8},{"year":2015,"cited_by_count":23},{"year":2014,"cited_by_count":23},{"year":2013,"cited_by_count":27},{"year":2012,"cited_by_count":15}],"updated_date":"2026-08-15T07:11:24.734988","created_date":"2025-10-10T00:00:00"}
