{"id":"https://openalex.org/W2052465173","doi":"https://doi.org/10.1021/ci050216q","title":"Symplectic Molecular Dynamics Simulations on Specially Designed Parallel Computers","display_name":"Symplectic Molecular Dynamics Simulations on Specially Designed Parallel Computers","publication_year":2005,"publication_date":"2005-10-12","ids":{"openalex":"https://openalex.org/W2052465173","doi":"https://doi.org/10.1021/ci050216q","mag":"2052465173","pmid":"https://pubmed.ncbi.nlm.nih.gov/16309260"},"language":"en","primary_location":{"id":"doi:10.1021/ci050216q","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci050216q","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5090213539","display_name":"Urban Bor\u0161tnik","orcid":null},"institutions":[{"id":"https://openalex.org/I4210152560","display_name":"National Institute of Chemistry","ror":"https://ror.org/050mac570","country_code":"SI","type":"facility","lineage":["https://openalex.org/I4210152560"]}],"countries":["SI"],"is_corresponding":false,"raw_author_name":"Urban Bor\u0161tnik","raw_affiliation_strings":["National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia","institution_ids":["https://openalex.org/I4210152560"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074495088","display_name":"Du\u0161anka Jane\u017ei\u010d","orcid":"https://orcid.org/0000-0003-4067-0116"},"institutions":[{"id":"https://openalex.org/I4210152560","display_name":"National Institute of Chemistry","ror":"https://ror.org/050mac570","country_code":"SI","type":"facility","lineage":["https://openalex.org/I4210152560"]}],"countries":["SI"],"is_corresponding":false,"raw_author_name":"Du\u0161anka Jane\u017ei\u010d","raw_affiliation_strings":["National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia","institution_ids":["https://openalex.org/I4210152560"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I4210152560"],"apc_list":null,"apc_paid":null,"fwci":62.7315,"has_fulltext":false,"cited_by_count":21,"citation_normalized_percentile":{"value":0.99564575,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"45","issue":"6","first_page":"1600","last_page":"1604"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11367","display_name":"Particle accelerators and beam dynamics","score":0.9977999925613403,"subfield":{"id":"https://openalex.org/subfields/2202","display_name":"Aerospace Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11367","display_name":"Particle accelerators and beam dynamics","score":0.9977999925613403,"subfield":{"id":"https://openalex.org/subfields/2202","display_name":"Aerospace Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10037","display_name":"Physics of Superconductivity and Magnetism","score":0.9909999966621399,"subfield":{"id":"https://openalex.org/subfields/3104","display_name":"Condensed Matter Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11809","display_name":"Advanced NMR Techniques and Applications","score":0.9886999726295471,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.751987099647522},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.7267391681671143},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.5741760730743408},{"id":"https://openalex.org/keywords/motion","display_name":"Motion (physics)","score":0.5055861473083496},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.47101983428001404},{"id":"https://openalex.org/keywords/dynamics","display_name":"Dynamics (music)","score":0.4360070526599884},{"id":"https://openalex.org/keywords/simulation","display_name":"Simulation","score":0.3661491870880127},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.13125398755073547},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.12351185083389282},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.10584640502929688},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.1013856828212738}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.751987099647522},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.7267391681671143},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.5741760730743408},{"id":"https://openalex.org/C104114177","wikidata":"https://www.wikidata.org/wiki/Q79782","display_name":"Motion (physics)","level":2,"score":0.5055861473083496},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.47101983428001404},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.4360070526599884},{"id":"https://openalex.org/C44154836","wikidata":"https://www.wikidata.org/wiki/Q45045","display_name":"Simulation","level":1,"score":0.3661491870880127},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.13125398755073547},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.12351185083389282},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.10584640502929688},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.1013856828212738},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004563","descriptor_name":"Electrochemistry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004563","descriptor_name":"Electrochemistry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004563","descriptor_name":"Electrochemistry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci050216q","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci050216q","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:16309260","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16309260","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":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W1966130600","https://openalex.org/W1968922060","https://openalex.org/W1975989612","https://openalex.org/W1986288466","https://openalex.org/W1986565442","https://openalex.org/W2009314081","https://openalex.org/W2013470095","https://openalex.org/W2014444014","https://openalex.org/W2050273205","https://openalex.org/W2056865774","https://openalex.org/W2062446822","https://openalex.org/W2066801815","https://openalex.org/W2072614030","https://openalex.org/W2074757120","https://openalex.org/W2084367325","https://openalex.org/W2092322205","https://openalex.org/W2093151204","https://openalex.org/W2103734924","https://openalex.org/W2124555222","https://openalex.org/W2323178299","https://openalex.org/W2492693090","https://openalex.org/W4234347480"],"related_works":["https://openalex.org/W2023156907","https://openalex.org/W1968806281","https://openalex.org/W3095515585","https://openalex.org/W3094899115","https://openalex.org/W4315498887","https://openalex.org/W4378377190","https://openalex.org/W1929120455","https://openalex.org/W2753556613","https://openalex.org/W2088034942","https://openalex.org/W2405661381"],"abstract_inverted_index":{"We":[0,95],"have":[1],"developed":[2],"a":[3,111,142],"computer":[4],"program":[5],"for":[6],"molecular":[7,104],"dynamics":[8],"(MD)":[9],"simulation":[10,49,70,102],"that":[11,79],"implements":[12],"the":[13,34,45,65,97,120,133],"Split":[14],"Integration":[15],"Symplectic":[16],"Method":[17],"(SISM)":[18],"and":[19,42,84,89,109],"is":[20,31,55,82,127],"designed":[21,60],"to":[22,113,131,139],"run":[23],"on":[24,58,106],"specialized":[25,107,124],"parallel":[26,61,125],"computers.":[27,116],"The":[28,52,73,117],"MD":[29,93,101,136],"integration":[30],"performed":[32],"by":[33],"SISM,":[35],"which":[36,63],"analytically":[37],"treats":[38],"high-frequency":[39],"vibrational":[40],"motion":[41,54],"thus":[43],"enables":[44,91],"use":[46],"of":[47,68,75,100,103,119,135],"longer":[48],"time":[50,67,71,81],"steps.":[51],"low-frequency":[53],"treated":[56],"numerically":[57],"specially":[59],"computers,":[62],"decreases":[64],"computational":[66,98],"each":[69],"step.":[72],"combination":[74,118],"these":[76],"approaches":[77],"means":[78],"less":[80],"required":[83],"fewer":[85],"steps":[86],"are":[87],"needed":[88],"so":[90],"fast":[92],"simulations.":[94],"study":[96],"performance":[99],"systems":[105],"computers":[108,126],"provide":[110],"comparison":[112],"standard":[114],"personal":[115],"SISM":[121],"with":[122],"two":[123],"an":[128],"effective":[129],"way":[130],"increase":[132],"speed":[134],"simulations":[137],"up":[138],"16-fold":[140],"over":[141],"single":[143],"PC":[144],"processor.":[145]},"counts_by_year":[{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2012,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}