{"id":"https://openalex.org/W2528003530","doi":"https://doi.org/10.1007/978-3-319-46079-6_14","title":"Early Experiences Porting the NAMD and VMD Molecular Simulation and Analysis Software to GPU-Accelerated OpenPOWER Platforms","display_name":"Early Experiences Porting the NAMD and VMD Molecular Simulation and Analysis Software to GPU-Accelerated OpenPOWER Platforms","publication_year":2016,"publication_date":"2016-01-01","ids":{"openalex":"https://openalex.org/W2528003530","doi":"https://doi.org/10.1007/978-3-319-46079-6_14","mag":"2528003530","pmid":"https://pubmed.ncbi.nlm.nih.gov/29202130"},"language":"en","primary_location":{"id":"doi:10.1007/978-3-319-46079-6_14","is_oa":false,"landing_page_url":"https://doi.org/10.1007/978-3-319-46079-6_14","pdf_url":null,"source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5710845","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5048680880","display_name":"John E. Stone","orcid":"https://orcid.org/0000-0001-7215-762X"},"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"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"John E. Stone","raw_affiliation_strings":["Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign","Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA"],"affiliations":[{"raw_affiliation_string":"Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003235488","display_name":"Antti-Pekka Hynninen","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":"Antti-Pekka Hynninen","raw_affiliation_strings":["Oak Ridge Leadership Computing Facility, Oak Ridge National Laboratory","Oak Ridge Leadership Computing Facility, Oak Ridge National Laboratory, Oak Ridge, TN, USA"],"affiliations":[{"raw_affiliation_string":"Oak Ridge Leadership Computing Facility, Oak Ridge National Laboratory","institution_ids":["https://openalex.org/I1289243028"]},{"raw_affiliation_string":"Oak Ridge Leadership Computing Facility, Oak Ridge National Laboratory, Oak Ridge, TN, USA","institution_ids":["https://openalex.org/I1289243028"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056552672","display_name":"J. C. Phillips","orcid":"https://orcid.org/0000-0002-2296-3591"},"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James C. Phillips","raw_affiliation_strings":["Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign","Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA"],"affiliations":[{"raw_affiliation_string":"Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5113534986","display_name":"Klaus Schulten","orcid":null},"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Klaus Schulten","raw_affiliation_strings":["Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign","Department of Physics, University of Illinois at Urbana-Champaign","Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA"],"affiliations":[{"raw_affiliation_string":"Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"Department of Physics, University of Illinois at Urbana-Champaign","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA","institution_ids":["https://openalex.org/I157725225"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5048680880"],"corresponding_institution_ids":["https://openalex.org/I157725225"],"apc_list":{"value":5000,"currency":"EUR","value_usd":5392},"apc_paid":null,"fwci":5.9133,"has_fulltext":false,"cited_by_count":40,"citation_normalized_percentile":{"value":0.96555351,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"9945","issue":null,"first_page":"188","last_page":"206"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9994000196456909,"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":0.9994000196456909,"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/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.9932000041007996,"subfield":{"id":"https://openalex.org/subfields/1708","display_name":"Hardware and Architecture"},"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/T11162","display_name":"Enzyme Structure and Function","score":0.9879000186920166,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/porting","display_name":"Porting","score":0.8951225876808167},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8611012697219849},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.6558037400245667},{"id":"https://openalex.org/keywords/compiler","display_name":"Compiler","score":0.603387176990509},{"id":"https://openalex.org/keywords/intrinsics","display_name":"Intrinsics","score":0.5485162138938904},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.5207517147064209},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.4807267487049103},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4600967764854431},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.3588779866695404},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.32373201847076416},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2342625856399536},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.16261029243469238},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.09222909808158875}],"concepts":[{"id":"https://openalex.org/C106251023","wikidata":"https://www.wikidata.org/wiki/Q851989","display_name":"Porting","level":3,"score":0.8951225876808167},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8611012697219849},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6558037400245667},{"id":"https://openalex.org/C169590947","wikidata":"https://www.wikidata.org/wiki/Q47506","display_name":"Compiler","level":2,"score":0.603387176990509},{"id":"https://openalex.org/C2908650547","wikidata":"https://www.wikidata.org/wiki/Q20999234","display_name":"Intrinsics","level":2,"score":0.5485162138938904},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.5207517147064209},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.4807267487049103},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4600967764854431},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.3588779866695404},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.32373201847076416},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2342625856399536},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.16261029243469238},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.09222909808158875},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1007/978-3-319-46079-6_14","is_oa":false,"landing_page_url":"https://doi.org/10.1007/978-3-319-46079-6_14","pdf_url":null,"source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},{"id":"pmid:29202130","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29202130","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"High performance computing : 31st International Conference, ISC High Performance 2016, Frankfurt, Germany, June 19-23, 2016, Proceedings. ISC High Performance (Conference) (31st : 2016 : Frankfurt, Germany)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:5710845","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5710845","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"High Perform Comput (2016)","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:5710845","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5710845","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"High Perform Comput (2016)","raw_type":"Text"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","score":0.47999998927116394,"display_name":"Affordable and clean energy"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W836966646","https://openalex.org/W1573103858","https://openalex.org/W1981115969","https://openalex.org/W2004383436","https://openalex.org/W2004822259","https://openalex.org/W2011205359","https://openalex.org/W2021064626","https://openalex.org/W2028499920","https://openalex.org/W2029667189","https://openalex.org/W2035687084","https://openalex.org/W2036381880","https://openalex.org/W2048346240","https://openalex.org/W2050513283","https://openalex.org/W2067174909","https://openalex.org/W2067571096","https://openalex.org/W2067635581","https://openalex.org/W2082211440","https://openalex.org/W2102927018","https://openalex.org/W2134600600","https://openalex.org/W2150981663","https://openalex.org/W2160544821","https://openalex.org/W2167173222","https://openalex.org/W2199743453","https://openalex.org/W2289084400","https://openalex.org/W2397547384","https://openalex.org/W2408504433","https://openalex.org/W2478973235","https://openalex.org/W2479768743","https://openalex.org/W2482361190","https://openalex.org/W2494083433","https://openalex.org/W3138798301","https://openalex.org/W3141032579","https://openalex.org/W4251841159"],"related_works":["https://openalex.org/W2356602486","https://openalex.org/W1987577928","https://openalex.org/W2351992668","https://openalex.org/W2324828474","https://openalex.org/W2374315191","https://openalex.org/W1987014004","https://openalex.org/W4313423325","https://openalex.org/W2013156670","https://openalex.org/W2088034942","https://openalex.org/W4390503633"],"abstract_inverted_index":null,"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":10},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":4},{"year":2016,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
