{"id":"https://openalex.org/W3116759281","doi":"https://doi.org/10.14529/jsfi180414","title":"Performance Analysis of Different Computational Architectures: Molecular Dynamics in Application to Protein Assemblies, Illustrated by Microtubule and Electron Transfer Proteins","display_name":"Performance Analysis of Different Computational Architectures: Molecular Dynamics in Application to Protein Assemblies, Illustrated by Microtubule and Electron Transfer Proteins","publication_year":2018,"publication_date":"2018-12-01","ids":{"openalex":"https://openalex.org/W3116759281","doi":"https://doi.org/10.14529/jsfi180414","mag":"3116759281"},"language":"en","primary_location":{"id":"doi:10.14529/jsfi180414","is_oa":true,"landing_page_url":"https://doi.org/10.14529/jsfi180414","pdf_url":"https://superfri.org/superfri/article/download/244/315","source":{"id":"https://openalex.org/S4210177204","display_name":"Supercomputing Frontiers and Innovations","issn_l":"2313-8734","issn":["2313-8734","2409-6008"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310312680","host_organization_name":"Publishing center of the South Ural State University","host_organization_lineage":["https://openalex.org/P4310312680"],"host_organization_lineage_names":["Publishing center of the South Ural State University"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Supercomputing Frontiers and Innovations","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://superfri.org/superfri/article/download/244/315","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064047524","display_name":"Vladimir A. Fedorov","orcid":"https://orcid.org/0000-0002-9397-1548"},"institutions":[{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Vladimir A. Fedorov","raw_affiliation_strings":["Lomonosov Moscow State University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lomonosov Moscow State University","institution_ids":["https://openalex.org/I19880235"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063796317","display_name":"Ekaterina G. Kholina","orcid":"https://orcid.org/0000-0002-5918-5084"},"institutions":[{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Ekaterina G. Kholina","raw_affiliation_strings":["Lomonosov Moscow State University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lomonosov Moscow State University","institution_ids":["https://openalex.org/I19880235"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003211987","display_name":"I. B. Kovalenko","orcid":"https://orcid.org/0000-0002-4949-6591"},"institutions":[{"id":"https://openalex.org/I178165815","display_name":"Astrakhan Tatischev State University","ror":"https://ror.org/04tf3kx07","country_code":"RU","type":"education","lineage":["https://openalex.org/I178165815"]},{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]},{"id":"https://openalex.org/I4210112215","display_name":"Astrakhan State Medical University","ror":"https://ror.org/01yvmh709","country_code":"RU","type":"education","lineage":["https://openalex.org/I4210112215"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Ilya B. Kovalenko","raw_affiliation_strings":["Lomonosov Moscow State University, Moscow, Russia\r\nFederal Research and Clinical Center of Specialized Medical Care and Medical Technologies, Federal Medical and Biological Agency of Russia, Moscow, Russia\r\nAstrakhan State University, Astrakhan, Russia\r\nScientic and Technological Center of Unique Instrumentation of the Russian Academy of Sciences, Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lomonosov Moscow State University, Moscow, Russia\r\nFederal Research and Clinical Center of Specialized Medical Care and Medical Technologies, Federal Medical and Biological Agency of Russia, Moscow, Russia\r\nAstrakhan State University, Astrakhan, Russia\r\nScientic and Technological Center of Unique Instrumentation of the Russian Academy of Sciences, Moscow, Russia","institution_ids":["https://openalex.org/I178165815","https://openalex.org/I19880235","https://openalex.org/I4210112215"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5071743188","display_name":"Nikita B. Gudimchuk","orcid":"https://orcid.org/0000-0002-7283-8959"},"institutions":[{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]},{"id":"https://openalex.org/I4210122842","display_name":"Center for Theoretical Problems of Physicochemical Pharmacology","ror":"https://ror.org/02ncvqp37","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210115279","https://openalex.org/I4210122842"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Nikita B. Gudimchuk","raw_affiliation_strings":["Lomonosov Moscow State University, Moscow, Russia\r\nCenter for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lomonosov Moscow State University, Moscow, Russia\r\nCenter for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, Moscow, Russia","institution_ids":["https://openalex.org/I19880235","https://openalex.org/I4210122842"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.2478,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.5422295,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"5","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10303","display_name":"Photosynthetic Processes and Mechanisms","score":0.9955000281333923,"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/T10303","display_name":"Photosynthetic Processes and Mechanisms","score":0.9955000281333923,"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/T10913","display_name":"Molecular Junctions and Nanostructures","score":0.9947999715805054,"subfield":{"id":"https://openalex.org/subfields/2208","display_name":"Electrical and Electronic 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/T10044","display_name":"Protein Structure and Dynamics","score":0.9930999875068665,"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/microtubule","display_name":"Microtubule","score":0.7239125967025757},{"id":"https://openalex.org/keywords/electron-transfer","display_name":"Electron transfer","score":0.5819380283355713},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.5626104474067688},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.4880620241165161},{"id":"https://openalex.org/keywords/dynamics","display_name":"Dynamics (music)","score":0.46497392654418945},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3865947127342224},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3802652955055237},{"id":"https://openalex.org/keywords/nanotechnology","display_name":"Nanotechnology","score":0.35947656631469727},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3403806984424591},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.33104878664016724},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.32767653465270996},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.30479490756988525},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.29686301946640015},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.22379741072654724},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2083301842212677},{"id":"https://openalex.org/keywords/physical-chemistry","display_name":"Physical chemistry","score":0.06228247284889221}],"concepts":[{"id":"https://openalex.org/C20418707","wikidata":"https://www.wikidata.org/wiki/Q189933","display_name":"Microtubule","level":2,"score":0.7239125967025757},{"id":"https://openalex.org/C123669783","wikidata":"https://www.wikidata.org/wiki/Q902898","display_name":"Electron transfer","level":2,"score":0.5819380283355713},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.5626104474067688},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.4880620241165161},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.46497392654418945},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3865947127342224},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3802652955055237},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.35947656631469727},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3403806984424591},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.33104878664016724},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32767653465270996},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.30479490756988525},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.29686301946640015},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.22379741072654724},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2083301842212677},{"id":"https://openalex.org/C147789679","wikidata":"https://www.wikidata.org/wiki/Q11372","display_name":"Physical chemistry","level":1,"score":0.06228247284889221},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.14529/jsfi180414","is_oa":true,"landing_page_url":"https://doi.org/10.14529/jsfi180414","pdf_url":"https://superfri.org/superfri/article/download/244/315","source":{"id":"https://openalex.org/S4210177204","display_name":"Supercomputing Frontiers and Innovations","issn_l":"2313-8734","issn":["2313-8734","2409-6008"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310312680","host_organization_name":"Publishing center of the South Ural State University","host_organization_lineage":["https://openalex.org/P4310312680"],"host_organization_lineage_names":["Publishing center of the South Ural State University"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Supercomputing Frontiers and Innovations","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.14529/jsfi180414","is_oa":true,"landing_page_url":"https://doi.org/10.14529/jsfi180414","pdf_url":"https://superfri.org/superfri/article/download/244/315","source":{"id":"https://openalex.org/S4210177204","display_name":"Supercomputing Frontiers and Innovations","issn_l":"2313-8734","issn":["2313-8734","2409-6008"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310312680","host_organization_name":"Publishing center of the South Ural State University","host_organization_lineage":["https://openalex.org/P4310312680"],"host_organization_lineage_names":["Publishing center of the South Ural State University"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Supercomputing Frontiers and Innovations","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Clean water and sanitation","score":0.550000011920929,"id":"https://metadata.un.org/sdg/6"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":3,"referenced_works":["https://openalex.org/W1031578623","https://openalex.org/W1895692106","https://openalex.org/W2493946584"],"related_works":["https://openalex.org/W2900684760","https://openalex.org/W2114542479","https://openalex.org/W2054976643","https://openalex.org/W2073057352","https://openalex.org/W2473195300","https://openalex.org/W2064422190","https://openalex.org/W4210494266","https://openalex.org/W2057381363","https://openalex.org/W2071528423","https://openalex.org/W2750958300"],"abstract_inverted_index":{"All-atom":[0],"molecular":[1,33,89,127,154],"dynamics":[2,34,90,128,155],"simulation":[3,156],"represents":[4],"a":[5],"computationally":[6],"challenging,":[7],"but":[8],"powerful":[9],"approach":[10],"for":[11,66,146,152],"studying":[12],"conformational":[13],"changes":[14],"and":[15,19,54,74,80,94,116],"interactions":[16],"of":[17,22,28,41,68,71,82,92,110,113,123,130,148],"biomolecules":[18],"their":[20],"assemblies":[21],"different":[23,72,96,131],"kinds.":[24],"Usually,":[25],"the":[26,44,62],"numbers":[27],"simulated":[29,45],"particles":[30],"in":[31,99,126,134],"modern":[32,114],"studies":[35],"range":[36],"from":[37,48],"thousands":[38],"to":[39,50,60],"tens":[40],"millions,":[42],"while":[43],"timescales":[46],"span":[47],"nanoseconds":[49,135],"microseconds.":[51],"For":[52],"cost":[53],"computation":[55],"efficiency,":[56],"it":[57],"is":[58],"important":[59],"determine":[61],"optimal":[63,149],"computer":[64,150],"hardware":[65,151],"simulations":[67,91,129],"biomolecular":[69],"systems":[70,98,133],"size":[73],"timescale.":[75],"Here":[76],"we":[77],"compare":[78],"performance":[79,109,122],"scalability":[81],"17":[83],"commercially":[84],"available":[85],"computational":[86],"architectures,":[87],"using":[88],"water":[93],"two":[95],"protein":[97,132],"GROMACS-5":[100],"package":[101],"as":[102,118,120,143],"computing":[103],"benchmarks.":[104],"We":[105],"report":[106],"typical":[107],"single-node":[108],"various":[111,153],"combinations":[112],"CPUs":[115],"GPUs,":[117],"well":[119],"multiple-node":[121],"\"Lomonosov-2\"":[124],"supercomputer":[125],"per":[136],"day.":[137],"These":[138],"data":[139],"can":[140],"be":[141],"used":[142],"practical":[144],"guidelines":[145],"selection":[147],"tasks.":[157]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1}],"updated_date":"2026-08-06T08:24:18.245995","created_date":"2021-01-05T00:00:00"}