{"id":"https://openalex.org/W2121224790","doi":"https://doi.org/10.1002/jcc.21035","title":"Application of MDGRAPE\u20103, a special purpose board for molecular dynamics simulations, to periodic biomolecular systems","display_name":"Application of MDGRAPE\u20103, a special purpose board for molecular dynamics simulations, to periodic biomolecular systems","publication_year":2008,"publication_date":"2008-06-04","ids":{"openalex":"https://openalex.org/W2121224790","doi":"https://doi.org/10.1002/jcc.21035","mag":"2121224790","pmid":"https://pubmed.ncbi.nlm.nih.gov/18524021"},"language":"en","primary_location":{"id":"doi:10.1002/jcc.21035","is_oa":false,"landing_page_url":"https://doi.org/10.1002/jcc.21035","pdf_url":null,"source":{"id":"https://openalex.org/S21117631","display_name":"Journal of Computational Chemistry","issn_l":"0192-8651","issn":["0192-8651","1096-987X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Chemistry","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/A5049168876","display_name":"Gota Kikugawa","orcid":"https://orcid.org/0000-0002-8145-8309"},"institutions":[{"id":"https://openalex.org/I4210165842","display_name":"RIKEN Center for Advanced Photonics","ror":"https://ror.org/05vmjks78","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210165842"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Gota Kikugawa","raw_affiliation_strings":["Advanced Center for Computing and Communication, RIKEN, 2-1, Hirosawa, Wako, Saitama 351-0198, Japan","Advanced Center for Computing and Communication, RIKEN, 2\u20101, Hirosawa, Wako, Saitama 351\u20100198, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Advanced Center for Computing and Communication, RIKEN, 2-1, Hirosawa, Wako, Saitama 351-0198, Japan","institution_ids":["https://openalex.org/I4210165842"]},{"raw_affiliation_string":"Advanced Center for Computing and Communication, RIKEN, 2\u20101, Hirosawa, Wako, Saitama 351\u20100198, Japan","institution_ids":["https://openalex.org/I4210165842"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009536511","display_name":"Rossen Apostolov","orcid":null},"institutions":[{"id":"https://openalex.org/I98285908","display_name":"The University of Osaka","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Rossen Apostolov","raw_affiliation_strings":["Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan","Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan","institution_ids":["https://openalex.org/I98285908"]},{"raw_affiliation_string":"Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan","institution_ids":["https://openalex.org/I98285908"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065783054","display_name":"Narutoshi Kamiya","orcid":"https://orcid.org/0000-0002-0527-6968"},"institutions":[{"id":"https://openalex.org/I98285908","display_name":"The University of Osaka","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Narutoshi Kamiya","raw_affiliation_strings":["Center for Advanced Medical Engineering and Informatics, Open Laboratories for Advanced Biosicence and Biotechnology, Osaka University, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan","Center for Advanced Medical Engineering and Informatics, Open Laboratories for Advanced Biosicence and Biotechnology, Osaka University, 6\u20102\u20103 Furuedai, Suita, Osaka 565\u20100874, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Advanced Medical Engineering and Informatics, Open Laboratories for Advanced Biosicence and Biotechnology, Osaka University, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan","institution_ids":["https://openalex.org/I98285908"]},{"raw_affiliation_string":"Center for Advanced Medical Engineering and Informatics, Open Laboratories for Advanced Biosicence and Biotechnology, Osaka University, 6\u20102\u20103 Furuedai, Suita, Osaka 565\u20100874, Japan","institution_ids":["https://openalex.org/I98285908"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033083222","display_name":"Makoto Taiji","orcid":"https://orcid.org/0000-0002-5317-0500"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Makoto Taiji","raw_affiliation_strings":["High Performance Biocomputing Research Team, Bioinformatics Group, Genomic, Sciences Center, RIKEN, 61-1 Onocho, Tsurumi, Yokohama, Kanagawa 230-0046, Japan","High Performance Biocomputing Research Team, Bioinformatics Group, Genomic, Sciences Center, RIKEN, 61\u20101 Onocho, Tsurumi, Yokohama, Kanagawa 230\u20100046, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"High Performance Biocomputing Research Team, Bioinformatics Group, Genomic, Sciences Center, RIKEN, 61-1 Onocho, Tsurumi, Yokohama, Kanagawa 230-0046, Japan","institution_ids":[]},{"raw_affiliation_string":"High Performance Biocomputing Research Team, Bioinformatics Group, Genomic, Sciences Center, RIKEN, 61\u20101 Onocho, Tsurumi, Yokohama, Kanagawa 230\u20100046, Japan","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091251386","display_name":"Ryutaro Himeno","orcid":"https://orcid.org/0000-0003-3378-6989"},"institutions":[{"id":"https://openalex.org/I4210165842","display_name":"RIKEN Center for Advanced Photonics","ror":"https://ror.org/05vmjks78","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210165842"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Ryutaro Himeno","raw_affiliation_strings":["Advanced Center for Computing and Communication, RIKEN, 2-1, Hirosawa, Wako, Saitama 351-0198, Japan","Advanced Center for Computing and Communication, RIKEN, 2\u20101, Hirosawa, Wako, Saitama 351\u20100198, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Advanced Center for Computing and Communication, RIKEN, 2-1, Hirosawa, Wako, Saitama 351-0198, Japan","institution_ids":["https://openalex.org/I4210165842"]},{"raw_affiliation_string":"Advanced Center for Computing and Communication, RIKEN, 2\u20101, Hirosawa, Wako, Saitama 351\u20100198, Japan","institution_ids":["https://openalex.org/I4210165842"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035143113","display_name":"Haruki Nakamura","orcid":"https://orcid.org/0000-0001-6690-5863"},"institutions":[{"id":"https://openalex.org/I98285908","display_name":"The University of Osaka","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Haruki Nakamura","raw_affiliation_strings":["Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan","Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan","institution_ids":["https://openalex.org/I98285908"]},{"raw_affiliation_string":"Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan","institution_ids":["https://openalex.org/I98285908"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5057742290","display_name":"Yasushige Yonezawa","orcid":"https://orcid.org/0000-0002-7794-7708"},"institutions":[{"id":"https://openalex.org/I98285908","display_name":"The University of Osaka","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Yasushige Yonezawa","raw_affiliation_strings":["Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan","Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan","institution_ids":["https://openalex.org/I98285908"]},{"raw_affiliation_string":"Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan","institution_ids":["https://openalex.org/I98285908"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5057742290"],"corresponding_institution_ids":["https://openalex.org/I98285908"],"apc_list":{"value":4840,"currency":"USD","value_usd":4840},"apc_paid":null,"fwci":1.667,"has_fulltext":false,"cited_by_count":50,"citation_normalized_percentile":{"value":0.83480304,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"30","issue":"1","first_page":"110","last_page":"118"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.996399998664856,"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.996399998664856,"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":0.9936000108718872,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9689000248908997,"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/periodic-boundary-conditions","display_name":"Periodic boundary conditions","score":0.8515852689743042},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.8207302093505859},{"id":"https://openalex.org/keywords/ewald-summation","display_name":"Ewald summation","score":0.6136535406112671},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.5742998719215393},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.5734150409698486},{"id":"https://openalex.org/keywords/range","display_name":"Range (aeronautics)","score":0.5417653918266296},{"id":"https://openalex.org/keywords/series","display_name":"Series (stratigraphy)","score":0.5381197929382324},{"id":"https://openalex.org/keywords/cutoff","display_name":"Cutoff","score":0.5194441676139832},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.49067986011505127},{"id":"https://openalex.org/keywords/particle-dynamics","display_name":"Particle dynamics","score":0.439645379781723},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.43018919229507446},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.3945574462413788},{"id":"https://openalex.org/keywords/boundary-value-problem","display_name":"Boundary value problem","score":0.32411840558052063},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.22705402970314026},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.16534486413002014},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.140472412109375}],"concepts":[{"id":"https://openalex.org/C112675119","wikidata":"https://www.wikidata.org/wiki/Q2992284","display_name":"Periodic boundary conditions","level":3,"score":0.8515852689743042},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.8207302093505859},{"id":"https://openalex.org/C143551052","wikidata":"https://www.wikidata.org/wiki/Q2426155","display_name":"Ewald summation","level":3,"score":0.6136535406112671},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.5742998719215393},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.5734150409698486},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.5417653918266296},{"id":"https://openalex.org/C143724316","wikidata":"https://www.wikidata.org/wiki/Q312468","display_name":"Series (stratigraphy)","level":2,"score":0.5381197929382324},{"id":"https://openalex.org/C2778217198","wikidata":"https://www.wikidata.org/wiki/Q556977","display_name":"Cutoff","level":2,"score":0.5194441676139832},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.49067986011505127},{"id":"https://openalex.org/C2985906894","wikidata":"https://www.wikidata.org/wiki/Q15994658","display_name":"Particle dynamics","level":3,"score":0.439645379781723},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.43018919229507446},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.3945574462413788},{"id":"https://openalex.org/C182310444","wikidata":"https://www.wikidata.org/wiki/Q1332643","display_name":"Boundary value problem","level":2,"score":0.32411840558052063},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.22705402970314026},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.16534486413002014},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.140472412109375},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"score":0.0}],"mesh":[{"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":"D008051","descriptor_name":"Lipid Bilayers","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008051","descriptor_name":"Lipid Bilayers","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008051","descriptor_name":"Lipid Bilayers","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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}],"locations_count":2,"locations":[{"id":"doi:10.1002/jcc.21035","is_oa":false,"landing_page_url":"https://doi.org/10.1002/jcc.21035","pdf_url":null,"source":{"id":"https://openalex.org/S21117631","display_name":"Journal of Computational Chemistry","issn_l":"0192-8651","issn":["0192-8651","1096-987X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Chemistry","raw_type":"journal-article"},{"id":"pmid:18524021","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18524021","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 computational chemistry","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":19,"referenced_works":["https://openalex.org/W1975945758","https://openalex.org/W1976499671","https://openalex.org/W2010912149","https://openalex.org/W2017164460","https://openalex.org/W2023971144","https://openalex.org/W2024669398","https://openalex.org/W2035687084","https://openalex.org/W2056081735","https://openalex.org/W2058395018","https://openalex.org/W2066346371","https://openalex.org/W2067174909","https://openalex.org/W2068644111","https://openalex.org/W2085178810","https://openalex.org/W2086741044","https://openalex.org/W2089989244","https://openalex.org/W2122199548","https://openalex.org/W2136278162","https://openalex.org/W2150765263","https://openalex.org/W2162166182"],"related_works":["https://openalex.org/W2080664146","https://openalex.org/W1760201122","https://openalex.org/W4291318421","https://openalex.org/W2951983062","https://openalex.org/W3020905577","https://openalex.org/W1480785517","https://openalex.org/W4239906789","https://openalex.org/W2006345232","https://openalex.org/W2009696457","https://openalex.org/W1987487955"],"abstract_inverted_index":{"We":[0],"describe":[1],"the":[2,16,25,37,72,97,120,148,157,164],"application":[3],"of":[4,18,31,78,127,163],"a":[5,29,132,142],"special":[6],"purpose":[7],"board":[8,27],"for":[9],"molecular":[10,159],"dynamics":[11,162],"simulations,":[12],"named":[13],"MDGRAPE-3,":[14],"to":[15,35,53,70,85,125,155],"problem":[17],"simulating":[19],"periodic":[20,89,129],"bio-molecular":[21],"systems.":[22,165],"MDGRAPE-3":[23,134],"is":[24],"latest":[26],"in":[28,68,147],"series":[30],"hardware":[32],"accelerators":[33],"designed":[34],"calculate":[36],"nonbonding":[38],"long-range":[39],"interactions":[40,60,87],"much":[41],"more":[42],"rapidly":[43],"than":[44,141],"normal":[45],"processors.":[46],"So":[47],"far,":[48],"MDGRAPEs":[49],"were":[50,61,123],"mainly":[51],"applied":[52,124],"isolated":[54],"systems,":[55,82,131],"where":[56],"very":[57],"many":[58],"nonbonded":[59],"calculated":[62],"without":[63],"any":[64],"distance":[65,106],"cutoff.":[66],"However,":[67],"order":[69],"regulate":[71],"density":[73],"and":[74,102,108,161],"pressure":[75],"during":[76],"simulations":[77,126],"membrane":[79],"embedded":[80],"protein":[81],"one":[83],"has":[84],"evaluate":[86],"under":[88],"boundary":[90],"conditions.":[91],"For":[92],"this":[93],"purpose,":[94],"we":[95],"implemented":[96],"Particle-Mesh":[98],"Ewald":[99],"(PME)":[100],"method,":[101],"its":[103],"approximation":[104],"with":[105],"cutoffs":[107],"charge":[109],"neutrality":[110],"as":[111],"proposed":[112],"by":[113],"Wolf":[114],"et":[115],"al.,":[116],"using":[117],"MDGRAPE-3.":[118],"When":[119],"two":[121,128],"methods":[122,152],"biomolecular":[130],"single":[133,143],"achieved":[135],"30-40":[136],"times":[137,140],"faster":[138],"computation":[139],"conventional":[144],"processor":[145],"did":[146],"both":[149],"cases.":[150],"Both":[151],"are":[153],"shown":[154],"have":[156],"same":[158],"structures":[160]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":4},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":12}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}