{"id":"https://openalex.org/W2023443554","doi":"https://doi.org/10.1145/2335755.2335810","title":"Transforming molecular biology research through extreme acceleration of AMBER molecular dynamics simulations","display_name":"Transforming molecular biology research through extreme acceleration of AMBER molecular dynamics simulations","publication_year":2012,"publication_date":"2012-07-16","ids":{"openalex":"https://openalex.org/W2023443554","doi":"https://doi.org/10.1145/2335755.2335810","mag":"2023443554"},"language":"en","primary_location":{"id":"doi:10.1145/2335755.2335810","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2335755.2335810","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the eXtreme to the campus and beyond","raw_type":"proceedings-article"},"type":"conference-abstract","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/A5112785999","display_name":"Ross C. Walker","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ross C. Walker","raw_affiliation_strings":["University of California San Diego, Gilman Drive, La Jolla, CA","University of California, San Diego, Gilman Drive, La Jolla, CA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of California San Diego, Gilman Drive, La Jolla, CA","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"University of California, San Diego, Gilman Drive, La Jolla, CA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011127316","display_name":"Levi Pierce","orcid":"https://orcid.org/0009-0001-1433-9908"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Levi Pierce","raw_affiliation_strings":["University of California San Diego, Gilman Drive, La Jolla, CA","University of California, San Diego, Gilman Drive, La Jolla, CA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of California San Diego, Gilman Drive, La Jolla, CA","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"University of California, San Diego, Gilman Drive, La Jolla, CA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5110531912","display_name":"Romelia Salomon","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Romelia Salomon","raw_affiliation_strings":["University of California San Diego, Gilman Drive, La Jolla, CA","University of California, San Diego, Gilman Drive, La Jolla, CA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of California San Diego, Gilman Drive, La Jolla, CA","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"University of California, San Diego, Gilman Drive, La Jolla, CA","institution_ids":["https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I36258959"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"1"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.8673999905586243,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},"topics":[{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.8673999905586243,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.8102999925613403,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11268","display_name":"Light effects on plants","score":0.7695000171661377,"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":0.7254807949066162},{"id":"https://openalex.org/keywords/acceleration","display_name":"Acceleration","score":0.6581493616104126},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.6384886503219604},{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.6052445769309998},{"id":"https://openalex.org/keywords/graphics-processing-unit","display_name":"Graphics processing unit","score":0.48771533370018005},{"id":"https://openalex.org/keywords/cuda","display_name":"CUDA","score":0.48572641611099243},{"id":"https://openalex.org/keywords/suite","display_name":"Suite","score":0.4750159680843353},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.46345895528793335},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.4602019488811493},{"id":"https://openalex.org/keywords/workstation","display_name":"Workstation","score":0.4531167447566986},{"id":"https://openalex.org/keywords/millisecond","display_name":"Millisecond","score":0.4272356927394867},{"id":"https://openalex.org/keywords/general-purpose-computing-on-graphics-processing-units","display_name":"General-purpose computing on graphics processing units","score":0.42592933773994446},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.35387006402015686},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.1726149022579193},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.16603487730026245},{"id":"https://openalex.org/keywords/astronomy","display_name":"Astronomy","score":0.0978015661239624},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.09571433067321777},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.09338712692260742}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7254807949066162},{"id":"https://openalex.org/C117896860","wikidata":"https://www.wikidata.org/wiki/Q11376","display_name":"Acceleration","level":2,"score":0.6581493616104126},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.6384886503219604},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.6052445769309998},{"id":"https://openalex.org/C2779851693","wikidata":"https://www.wikidata.org/wiki/Q183484","display_name":"Graphics processing unit","level":2,"score":0.48771533370018005},{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.48572641611099243},{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.4750159680843353},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.46345895528793335},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.4602019488811493},{"id":"https://openalex.org/C67953723","wikidata":"https://www.wikidata.org/wiki/Q192525","display_name":"Workstation","level":2,"score":0.4531167447566986},{"id":"https://openalex.org/C60327585","wikidata":"https://www.wikidata.org/wiki/Q723733","display_name":"Millisecond","level":2,"score":0.4272356927394867},{"id":"https://openalex.org/C50630238","wikidata":"https://www.wikidata.org/wiki/Q971505","display_name":"General-purpose computing on graphics processing units","level":3,"score":0.42592933773994446},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.35387006402015686},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.1726149022579193},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.16603487730026245},{"id":"https://openalex.org/C1276947","wikidata":"https://www.wikidata.org/wiki/Q333","display_name":"Astronomy","level":1,"score":0.0978015661239624},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.09571433067321777},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.09338712692260742},{"id":"https://openalex.org/C74650414","wikidata":"https://www.wikidata.org/wiki/Q11397","display_name":"Classical mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/2335755.2335810","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2335755.2335810","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the eXtreme to the campus and beyond","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.46000000834465027,"display_name":"Clean water and sanitation","id":"https://metadata.un.org/sdg/6"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W1963859303","https://openalex.org/W2364044215","https://openalex.org/W2389600408","https://openalex.org/W240129890","https://openalex.org/W3048701459","https://openalex.org/W2149078538","https://openalex.org/W2080146221","https://openalex.org/W2370314112","https://openalex.org/W2153506571","https://openalex.org/W3104348697"],"abstract_inverted_index":{"This":[0],"talk":[1],"will":[2,26,138],"cover":[3],"recent":[4,29,44],"developments":[5,136],"in":[6,96,178],"the":[7,19,35,48,56,120,140,167],"acceleration":[8,141],"of":[9,52,64,77,112,142],"Molecular":[10],"Dynamics":[11],"Simulations":[12],"using":[13,123,146],"NVIDIA":[14],"Graphics":[15,129],"Processing":[16],"units":[17,149],"with":[18,73,102],"AMBER":[20,143],"software":[21],"package.":[22],"In":[23],"particular":[24],"it":[25,106],"focus":[27],"on":[28,82,119,194],"algorithmic":[30],"improvements":[31],"aimed":[32],"at":[33,37],"accelerating":[34],"rate":[36],"which":[38],"phase":[39],"space":[40],"is":[41,107],"sampled.":[42],"A":[43],"success":[45],"has":[46],"been":[47],"reproduction":[49],"and":[50,131,153,196],"extension":[51],"key":[53],"results":[54,99],"from":[55],"DE":[57],"Shaw":[58],"1":[59],"millisecond":[60,121],"Anton":[61],"MD":[62,144],"simulation":[63],"BPTI":[65],"(Science,":[66],"Vol.":[67],"330":[68],"no.":[69],"6002":[70],"pp.":[71],"341-346)":[72],"just":[74,124],"2.5":[75],"days":[76],"dihedral":[78],"boosted":[79],"AMD":[80],"sampling":[81,111],"a":[83,125,132,161],"single":[84,126],"GPU":[85,189],"workstation,":[86],"(Pierce":[87],"L,":[88],"Walker":[89],"R.":[90,172],"C.":[91,173],"et":[92,174],"al.":[93],"JCTC,":[94],"2012":[95],"review).":[97],"These":[98],"show":[100],"that":[101,117],"careful":[103],"algorithm":[104],"design":[105],"possible":[108],"to":[109],"obtain":[110],"rare":[113],"biologically":[114],"relevant":[115],"events":[116],"occur":[118],"timescale":[122],"$500":[127],"GTX580":[128],"Card":[130],"desktop":[133],"workstation.":[134],"Additional":[135],"highlighted":[137],"include":[139],"simulations":[145],"graphics":[147],"processing":[148],"including":[150],"Amazon":[151],"EC2":[152],"Microsoft":[154],"Azure":[155],"Cloud":[156],"based":[157],"automated":[158],"ensemble":[159],"calculations,":[160],"new":[162],"precision":[163],"model":[164],"optimized":[165],"for":[166,184],"upcoming":[168],"Kepler":[169],"architecture":[170],"(Walker":[171],"al,":[175],"JCP,":[176],"2012,":[177],"prep)":[179],"as":[180,182],"well":[181],"approaches":[183],"running":[185],"large":[186],"scale":[187],"multi-dimensional":[188],"accelerated":[190],"replica":[191],"exchange":[192],"calculations":[193],"Keeneland":[195],"BlueWaters.":[197]},"counts_by_year":[{"year":2015,"cited_by_count":1}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
