{"id":"https://openalex.org/W2119078084","doi":"https://doi.org/10.1145/1122971.1122983","title":"Performance characterization of molecular dynamics techniques for biomolecular simulations","display_name":"Performance characterization of molecular dynamics techniques for biomolecular simulations","publication_year":2006,"publication_date":"2006-03-29","ids":{"openalex":"https://openalex.org/W2119078084","doi":"https://doi.org/10.1145/1122971.1122983","mag":"2119078084"},"language":"en","primary_location":{"id":"doi:10.1145/1122971.1122983","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1122971.1122983","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the eleventh ACM SIGPLAN symposium on Principles and practice of parallel programming","raw_type":"proceedings-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/A5029432902","display_name":"Sadaf R. Alam","orcid":"https://orcid.org/0000-0002-2534-5078"},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sadaf R. Alam","raw_affiliation_strings":["Oak Ridge National Laboratory, Oak Ridge, TN","Oak Ridge National Laboratory, Oak Ridge, TN#TAB#"],"affiliations":[{"raw_affiliation_string":"Oak Ridge National Laboratory, Oak Ridge, TN","institution_ids":["https://openalex.org/I1289243028"]},{"raw_affiliation_string":"Oak Ridge National Laboratory, Oak Ridge, TN#TAB#","institution_ids":["https://openalex.org/I1289243028"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061838490","display_name":"Jeffrey S. Vetter","orcid":"https://orcid.org/0000-0002-2449-6720"},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeffrey S. Vetter","raw_affiliation_strings":["Oak Ridge National Laboratory, Oak Ridge, TN","Oak Ridge National Laboratory, Oak Ridge, TN#TAB#"],"affiliations":[{"raw_affiliation_string":"Oak Ridge National Laboratory, Oak Ridge, TN","institution_ids":["https://openalex.org/I1289243028"]},{"raw_affiliation_string":"Oak Ridge National Laboratory, Oak Ridge, TN#TAB#","institution_ids":["https://openalex.org/I1289243028"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053107527","display_name":"Pratul K. Agarwal","orcid":"https://orcid.org/0000-0002-3848-9492"},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Pratul K. Agarwal","raw_affiliation_strings":["Oak Ridge National Laboratory, Oak Ridge, TN","Oak Ridge National Laboratory, Oak Ridge, TN#TAB#"],"affiliations":[{"raw_affiliation_string":"Oak Ridge National Laboratory, Oak Ridge, TN","institution_ids":["https://openalex.org/I1289243028"]},{"raw_affiliation_string":"Oak Ridge National Laboratory, Oak Ridge, TN#TAB#","institution_ids":["https://openalex.org/I1289243028"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5113990568","display_name":"Al Geist","orcid":null},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Al Geist","raw_affiliation_strings":["Oak Ridge National Laboratory, Oak Ridge, TN","Oak Ridge National Laboratory, Oak Ridge, TN#TAB#"],"affiliations":[{"raw_affiliation_string":"Oak Ridge National Laboratory, Oak Ridge, TN","institution_ids":["https://openalex.org/I1289243028"]},{"raw_affiliation_string":"Oak Ridge National Laboratory, Oak Ridge, TN#TAB#","institution_ids":["https://openalex.org/I1289243028"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5029432902"],"corresponding_institution_ids":["https://openalex.org/I1289243028"],"apc_list":null,"apc_paid":null,"fwci":2.5168,"has_fulltext":false,"cited_by_count":27,"citation_normalized_percentile":{"value":0.89028802,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":null,"issue":null,"first_page":"59","last_page":"68"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9937000274658203,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9937000274658203,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9916999936103821,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9835000038146973,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7445970177650452},{"id":"https://openalex.org/keywords/massively-parallel","display_name":"Massively parallel","score":0.7345359325408936},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.7206360101699829},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.650723934173584},{"id":"https://openalex.org/keywords/scaling","display_name":"Scaling","score":0.5655953884124756},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.5389407873153687},{"id":"https://openalex.org/keywords/ibm","display_name":"IBM","score":0.5387405753135681},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.4925599694252014},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.4847557246685028},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.4396136701107025},{"id":"https://openalex.org/keywords/nanotechnology","display_name":"Nanotechnology","score":0.17121565341949463},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.1188456118106842},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.10810807347297668},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.09365463256835938},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.0894927978515625}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7445970177650452},{"id":"https://openalex.org/C190475519","wikidata":"https://www.wikidata.org/wiki/Q544384","display_name":"Massively parallel","level":2,"score":0.7345359325408936},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.7206360101699829},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.650723934173584},{"id":"https://openalex.org/C99844830","wikidata":"https://www.wikidata.org/wiki/Q102441924","display_name":"Scaling","level":2,"score":0.5655953884124756},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.5389407873153687},{"id":"https://openalex.org/C70388272","wikidata":"https://www.wikidata.org/wiki/Q5968558","display_name":"IBM","level":2,"score":0.5387405753135681},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.4925599694252014},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.4847557246685028},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.4396136701107025},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.17121565341949463},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.1188456118106842},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.10810807347297668},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.09365463256835938},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0894927978515625},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/1122971.1122983","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1122971.1122983","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the eleventh ACM SIGPLAN symposium on Principles and practice of parallel programming","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy","score":0.75}],"awards":[],"funders":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320338284","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63"},{"id":"https://openalex.org/F4320338287","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":25,"referenced_works":["https://openalex.org/W303505896","https://openalex.org/W1495469490","https://openalex.org/W1521042556","https://openalex.org/W1588517684","https://openalex.org/W1965351873","https://openalex.org/W1971952282","https://openalex.org/W2019465613","https://openalex.org/W2020346881","https://openalex.org/W2045583971","https://openalex.org/W2053792124","https://openalex.org/W2067174909","https://openalex.org/W2071789190","https://openalex.org/W2082912027","https://openalex.org/W2086037463","https://openalex.org/W2093381148","https://openalex.org/W2103815459","https://openalex.org/W2124099550","https://openalex.org/W2131025577","https://openalex.org/W2143784594","https://openalex.org/W2156879354","https://openalex.org/W2162166182","https://openalex.org/W2170396259","https://openalex.org/W4253069708","https://openalex.org/W4255916494","https://openalex.org/W6671299100"],"related_works":["https://openalex.org/W2251285835","https://openalex.org/W2073684863","https://openalex.org/W1582436825","https://openalex.org/W2167527468","https://openalex.org/W2586370661","https://openalex.org/W2314053740","https://openalex.org/W1996803181","https://openalex.org/W2979588510","https://openalex.org/W2960681633","https://openalex.org/W1970113381"],"abstract_inverted_index":{"Large-scale":[0],"simulations":[1,24],"and":[2,31,52,75,111,142,182,197,223,226,240],"computational":[3],"modeling":[4],"using":[5],"molecular":[6],"dynamics":[7],"(MD)":[8],"continues":[9],"to":[10,59,83,120,219],"make":[11,57],"significant":[12],"impacts":[13],"in":[14,202,295],"the":[15,97,105,108,121,136,150,164,171,179,184,190,206,230,236,243,246,252,278,288,297],"field":[16],"of":[17,25,39,61,63,70,87,96,107,124,157,160,245,256,300],"biology.":[18],"It":[19],"is":[20,232,259],"well":[21],"known":[22],"that":[23,134,204,229,251,271],"biological":[26,125,132,257],"events":[27],"at":[28],"native":[29],"time":[30],"length":[32],"scales":[33],"requires":[34],"computing":[35,64],"power":[36,65],"several":[37],"orders":[38],"magnitude":[40],"beyond":[41,208],"today's":[42],"commonly":[43],"available":[44,66,263],"systems.":[45],"Supercomputers,":[46],"such":[47],"as":[48],"IBM":[49],"Blue":[50,221],"Gene/L":[51,222],"Cray":[53],"XT3,":[54],"will":[55],"soon":[56],"tens":[58],"hundreds":[60],"teraFLOP/s":[62],"by":[67,235,242,261],"utilizing":[68],"thousands":[69,86],"processors.":[71,88,210],"The":[72],"popular":[73],"algorithms":[74,110],"MD":[76,137,272],"applications,":[77],"however,":[78],"were":[79],"not":[80],"initially":[81],"designed":[82],"run":[84],"on":[85,113,170,217],"In":[89,146,266],"this":[90],"paper,":[91],"we":[92,128,148,168,188,249],"present":[93],"detailed":[94],"investigations":[95],"performance":[98,213],"issues,":[99],"which":[100,153],"are":[101],"crucial":[102],"for":[103,177,183,215,290],"improving":[104],"scalability":[106],"MD-related":[109],"applications":[112],"massively":[114],"parallel":[115],"processing":[116],"(MPP)":[117],"architectures.":[118,303],"Due":[119],"varying":[122],"characteristics":[123,239],"input":[126,161,253],"problems,":[127],"study":[129,149],"two":[130],"prototypical":[131],"complexes":[133],"use":[135],"algorithm:":[138],"an":[139,143],"explicit":[140,165],"solvent":[141,166,186],"implicit":[144,185],"solvent.":[145],"particular,":[147],"AMBER":[151,203],"application,":[152],"supports":[154],"a":[155,200],"variety":[156],"these":[158,301],"types":[159],"problems.":[162],"For":[163],"problem,":[167],"focused":[169],"particle":[172],"mesh":[173],"Ewald":[174],"(PME)":[175],"method":[176],"calculating":[178],"electrostatic":[180],"energy,":[181],"model,":[187],"targeted":[189],"Generalized":[191],"Born":[192],"(GB)":[193],"calculation.":[194],"We":[195,211],"uncovered":[196],"subsequently":[198,227],"modified":[199],"limitation":[201],"restricted":[205],"scaling":[207,231],"128":[209],"collected":[212],"data":[214],"experiments":[216],"up":[218],"2048":[220],"XT3":[224],"processors":[225],"identified":[228],"largely":[233],"limited":[234],"underlying":[237],"algorithmic":[238],"also":[241],"implementation":[244],"algorithms.":[247],"Furthermore,":[248],"found":[250],"problem":[254],"size":[255],"system":[258],"constrained":[260],"memory":[262],"per":[264],"node.":[265],"conclusion,":[267],"our":[268],"results":[269],"indicate":[270],"codes":[273],"can":[274],"significantly":[275],"benefit":[276],"from":[277],"current":[279],"generation":[280],"architectures":[281],"with":[282],"relatively":[283],"modest":[284],"optimization":[285],"efforts.":[286],"Nevertheless,":[287],"key":[289],"enabling":[291],"scientific":[292],"breakthroughs":[293],"lies":[294],"exploiting":[296],"full":[298],"potential":[299],"new":[302]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
