{"id":"https://openalex.org/W4417173824","doi":"https://doi.org/10.1021/acs.jcim.5c02162","title":"GPU-Accelerated Implementation of Constant-pH Molecular Dynamics in NAMD","display_name":"GPU-Accelerated Implementation of Constant-pH Molecular Dynamics in NAMD","publication_year":2025,"publication_date":"2025-12-09","ids":{"openalex":"https://openalex.org/W4417173824","doi":"https://doi.org/10.1021/acs.jcim.5c02162","pmid":"https://pubmed.ncbi.nlm.nih.gov/41364919"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c02162","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c02162","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":true,"oa_status":"green","oa_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12756948/","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5026980055","display_name":"Sarah Moe","orcid":"https://orcid.org/0009-0009-1528-7079"},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sarah Moe","raw_affiliation_strings":["Department of Chemistry","The University of Chicago"],"raw_orcid":"https://orcid.org/0009-0009-1528-7079","affiliations":[{"raw_affiliation_string":"Department of Chemistry","institution_ids":[]},{"raw_affiliation_string":"The University of Chicago","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076283101","display_name":"Christophe Chipot","orcid":"https://orcid.org/0000-0002-9122-1698"},"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"]},{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]},{"id":"https://openalex.org/I4210089144","display_name":"Centre National pour la Recherche Scientifique et Technique (CNRST)","ror":"https://ror.org/00675rp98","country_code":"MA","type":"government","lineage":["https://openalex.org/I4210089144"]},{"id":"https://openalex.org/I4210125404","display_name":"Institute of Theoretical Physics","ror":"https://ror.org/02xtbq882","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210125404"]},{"id":"https://openalex.org/I90183372","display_name":"Universit\u00e9 de Lorraine","ror":"https://ror.org/04vfs2w97","country_code":"FR","type":"education","lineage":["https://openalex.org/I90183372"]}],"countries":["CN","FR","MA","US"],"is_corresponding":false,"raw_author_name":"Christophe Chipot","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology","Laboratoire International Associ\u00e9 Centre National de la Recherche Scientifique et University of Illinois at Urbana\u2212Champaign, Unit\u00e9 Mixte de Recherche No. 7019","The University of Chicago","Theoretical and Computational Biophysics Group, Beckman Institute, and Department of Physics","University of Illinois at Urbana\u2212Champaign","Universit\u00e9 de Lorraine"],"raw_orcid":"https://orcid.org/0000-0002-9122-1698","affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology","institution_ids":[]},{"raw_affiliation_string":"Laboratoire International Associ\u00e9 Centre National de la Recherche Scientifique et University of Illinois at Urbana\u2212Champaign, Unit\u00e9 Mixte de Recherche No. 7019","institution_ids":["https://openalex.org/I4210089144"]},{"raw_affiliation_string":"The University of Chicago","institution_ids":["https://openalex.org/I40347166"]},{"raw_affiliation_string":"Theoretical and Computational Biophysics Group, Beckman Institute, and Department of Physics","institution_ids":["https://openalex.org/I4210125404"]},{"raw_affiliation_string":"University of Illinois at Urbana\u2212Champaign","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"Universit\u00e9 de Lorraine","institution_ids":["https://openalex.org/I90183372"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5102778212","display_name":"Beno\u0131\u0302t Roux","orcid":"https://orcid.org/0000-0002-5254-2712"},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Beno\u00eet Roux","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology","Department of Chemistry","The University of Chicago"],"raw_orcid":"https://orcid.org/0000-0002-5254-2712","affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology","institution_ids":[]},{"raw_affiliation_string":"Department of Chemistry","institution_ids":[]},{"raw_affiliation_string":"The University of Chicago","institution_ids":["https://openalex.org/I40347166"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5102778212"],"corresponding_institution_ids":["https://openalex.org/I40347166"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.3364181,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"65","issue":"24","first_page":"13338","last_page":"13345"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.8300999999046326,"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":0.8300999999046326,"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/T11177","display_name":"Spectroscopy and Quantum Chemical Studies","score":0.02329999953508377,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"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/T11162","display_name":"Enzyme Structure and Function","score":0.014999999664723873,"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/speedup","display_name":"Speedup","score":0.796500027179718},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.7526000142097473},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.7095000147819519},{"id":"https://openalex.org/keywords/range","display_name":"Range (aeronautics)","score":0.52920001745224},{"id":"https://openalex.org/keywords/monte-carlo-method","display_name":"Monte Carlo method","score":0.4413999915122986},{"id":"https://openalex.org/keywords/qm/mm","display_name":"QM/MM","score":0.3718999922275543}],"concepts":[{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.796500027179718},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.7526000142097473},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7124000191688538},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.7095000147819519},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.52920001745224},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.44530001282691956},{"id":"https://openalex.org/C19499675","wikidata":"https://www.wikidata.org/wiki/Q232207","display_name":"Monte Carlo method","level":2,"score":0.4413999915122986},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.413100004196167},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4034000039100647},{"id":"https://openalex.org/C20803032","wikidata":"https://www.wikidata.org/wiki/Q207900","display_name":"QM/MM","level":3,"score":0.3718999922275543},{"id":"https://openalex.org/C74859849","wikidata":"https://www.wikidata.org/wiki/Q2466686","display_name":"Non-equilibrium thermodynamics","level":2,"score":0.36419999599456787},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.29109999537467957},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.28369998931884766},{"id":"https://openalex.org/C32848918","wikidata":"https://www.wikidata.org/wiki/Q845789","display_name":"Observable","level":2,"score":0.27799999713897705},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.2775000035762787},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.26030001044273376},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.2547000050544739}],"mesh":[{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006863","descriptor_name":"Hydrogen-Ion Concentration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006863","descriptor_name":"Hydrogen-Ion Concentration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006863","descriptor_name":"Hydrogen-Ion Concentration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006863","descriptor_name":"Hydrogen-Ion Concentration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011522","descriptor_name":"Protons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011522","descriptor_name":"Protons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011522","descriptor_name":"Protons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011522","descriptor_name":"Protons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.5c02162","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c02162","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:41364919","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41364919","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},{"id":"pmh:oai:pubmedcentral.nih.gov:12756948","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12756948/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:12756948","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12756948/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"J Chem Inf Model","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1435445245","display_name":null,"funder_award_id":"MCB-2309048","funder_id":"https://openalex.org/F4320337397","funder_display_name":"Division of Molecular and Cellular Biosciences"},{"id":"https://openalex.org/G4947865280","display_name":null,"funder_award_id":"1S10OD028655","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6027675088","display_name":null,"funder_award_id":"R35-GM152124","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337397","display_name":"Division of Molecular and Cellular Biosciences","ror":"https://ror.org/002jdaq33"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":86,"referenced_works":["https://openalex.org/W998400604","https://openalex.org/W1153842025","https://openalex.org/W1498352465","https://openalex.org/W1505374905","https://openalex.org/W1666053278","https://openalex.org/W1963882076","https://openalex.org/W1966225694","https://openalex.org/W1966623403","https://openalex.org/W1969189143","https://openalex.org/W1976499671","https://openalex.org/W1977482735","https://openalex.org/W1981603843","https://openalex.org/W1982276225","https://openalex.org/W1990902993","https://openalex.org/W1995141949","https://openalex.org/W1995160578","https://openalex.org/W1996734800","https://openalex.org/W1998486888","https://openalex.org/W2002507860","https://openalex.org/W2003312854","https://openalex.org/W2003451283","https://openalex.org/W2003516919","https://openalex.org/W2004223513","https://openalex.org/W2005006118","https://openalex.org/W2005423400","https://openalex.org/W2005679019","https://openalex.org/W2015233467","https://openalex.org/W2021534482","https://openalex.org/W2021820673","https://openalex.org/W2027408247","https://openalex.org/W2029899439","https://openalex.org/W2032427406","https://openalex.org/W2035432821","https://openalex.org/W2035687084","https://openalex.org/W2038758364","https://openalex.org/W2040008731","https://openalex.org/W2048727757","https://openalex.org/W2050447276","https://openalex.org/W2060297361","https://openalex.org/W2060872117","https://openalex.org/W2061438701","https://openalex.org/W2062630094","https://openalex.org/W2066070661","https://openalex.org/W2068815904","https://openalex.org/W2070144513","https://openalex.org/W2073275733","https://openalex.org/W2074225530","https://openalex.org/W2076407822","https://openalex.org/W2077168898","https://openalex.org/W2077221346","https://openalex.org/W2084346866","https://openalex.org/W2095213407","https://openalex.org/W2103125723","https://openalex.org/W2103945336","https://openalex.org/W2114764346","https://openalex.org/W2118171500","https://openalex.org/W2120269518","https://openalex.org/W2121529961","https://openalex.org/W2123147586","https://openalex.org/W2128629409","https://openalex.org/W2149801992","https://openalex.org/W2155163585","https://openalex.org/W2158667963","https://openalex.org/W2163168043","https://openalex.org/W2166478478","https://openalex.org/W2168269595","https://openalex.org/W2411825743","https://openalex.org/W2477513509","https://openalex.org/W2529068577","https://openalex.org/W2555870966","https://openalex.org/W2767829222","https://openalex.org/W2950447929","https://openalex.org/W2966054181","https://openalex.org/W3019212177","https://openalex.org/W3039216059","https://openalex.org/W3046751266","https://openalex.org/W3073482037","https://openalex.org/W3161639839","https://openalex.org/W4211031500","https://openalex.org/W4294146789","https://openalex.org/W4296700375","https://openalex.org/W4309094308","https://openalex.org/W4309564745","https://openalex.org/W4393378661","https://openalex.org/W4407246964","https://openalex.org/W4412929533"],"related_works":[],"abstract_inverted_index":{"We":[0],"introduce":[1],"a":[2,27,53,68,81,86],"GPU-based":[3],"implementation":[4,25],"of":[5,39,48,56,62,96],"the":[6,16,23,36,45,76],"hybrid":[7],"nonequilibrium":[8],"molecular":[9,73],"dynamics-Monte":[10],"Carlo":[11],"constant-pH":[12],"simulation":[13],"method":[14],"within":[15,71],"NAMD":[17],"package.":[18],"Benchmark":[19],"results":[20],"demonstrate":[21],"that":[22],"new":[24],"achieves":[26],"substantial":[28],"speedup":[29],"over":[30],"its":[31],"CPU-based":[32],"counterpart,":[33],"while":[34],"preserving":[35],"same":[37],"level":[38],"accuracy.":[40],"This":[41],"performance":[42],"gain":[43],"expands":[44],"practical":[46],"applicability":[47],"pH-controlled,":[49],"all-atom":[50],"simulations":[51],"across":[52],"wide":[54],"range":[55],"biomolecular":[57],"systems.":[58],"Although":[59],"exhaustive":[60],"enumeration":[61],"all":[63],"possible":[64],"protonation-state":[65],"combinations":[66],"remains":[67],"major":[69],"challenge":[70],"conventional":[72],"dynamics":[74],"frameworks,":[75],"ability":[77],"to":[78],"simulate":[79],"at":[80],"defined":[82],"pH\u2500combined":[83],"with":[84],"GPU-acceleration\u2500offers":[85],"powerful":[87],"and":[88],"efficient":[89],"means":[90],"for":[91],"investigating":[92],"dynamic":[93],"protonation":[94],"profiles":[95],"biomolecules.":[97]},"counts_by_year":[],"updated_date":"2025-12-23T23:11:35.936235","created_date":"2025-12-09T00:00:00"}