{"id":"https://openalex.org/W1997004261","doi":"https://doi.org/10.1002/(sici)1096-987x(199805)19:7<726::aid-jcc4>3.0.co;2-s","title":"The flying ice cube: Velocity rescaling in molecular dynamics leads to violation of energy equipartition","display_name":"The flying ice cube: Velocity rescaling in molecular dynamics leads to violation of energy equipartition","publication_year":1998,"publication_date":"1998-05-01","ids":{"openalex":"https://openalex.org/W1997004261","doi":"https://doi.org/10.1002/(sici)1096-987x(199805)19:7<726::aid-jcc4>3.0.co;2-s","mag":"1997004261"},"language":"en","primary_location":{"id":"doi:10.1002/(sici)1096-987x(199805)19:7<726::aid-jcc4>3.0.co;2-s","is_oa":false,"landing_page_url":"https://doi.org/10.1002/(sici)1096-987x(199805)19:7<726::aid-jcc4>3.0.co;2-s","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"],"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/A5088307660","display_name":"Stephen C. Harvey","orcid":"https://orcid.org/0000-0001-7073-6564"},"institutions":[{"id":"https://openalex.org/I32389192","display_name":"University of Alabama at Birmingham","ror":"https://ror.org/008s83205","country_code":"US","type":"education","lineage":["https://openalex.org/I32389192"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Stephen C. Harvey","raw_affiliation_strings":["Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35294"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35294","institution_ids":["https://openalex.org/I32389192"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110057296","display_name":"Robert K.\u2010Z. Tan","orcid":null},"institutions":[{"id":"https://openalex.org/I32389192","display_name":"University of Alabama at Birmingham","ror":"https://ror.org/008s83205","country_code":"US","type":"education","lineage":["https://openalex.org/I32389192"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert K.-Z. Tan","raw_affiliation_strings":["Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35294"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35294","institution_ids":["https://openalex.org/I32389192"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020579549","display_name":"Thomas E. Cheatham","orcid":"https://orcid.org/0000-0003-0298-3904"},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thomas E. Cheatham","raw_affiliation_strings":["Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143","Dept. of Pharmaceutical Chemistry, University of California, San Francisco, California 94143"],"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143","institution_ids":["https://openalex.org/I180670191"]},{"raw_affiliation_string":"Dept. of Pharmaceutical Chemistry, University of California, San Francisco, California 94143","institution_ids":["https://openalex.org/I180670191"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5088307660"],"corresponding_institution_ids":["https://openalex.org/I32389192"],"apc_list":{"value":4840,"currency":"USD","value_usd":4840},"apc_paid":null,"fwci":4.1968,"has_fulltext":false,"cited_by_count":399,"citation_normalized_percentile":{"value":0.94868847,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"19","issue":"7","first_page":"726","last_page":"740"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9993000030517578,"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":0.9993000030517578,"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/T11582","display_name":"Nanopore and Nanochannel Transport Studies","score":0.9973999857902527,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical 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":0.9926000237464905,"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/degrees-of-freedom","display_name":"Degrees of freedom (physics and chemistry)","score":0.7733912467956543},{"id":"https://openalex.org/keywords/kinetic-energy","display_name":"Kinetic energy","score":0.7682518362998962},{"id":"https://openalex.org/keywords/equipartition-theorem","display_name":"Equipartition theorem","score":0.7526895403862},{"id":"https://openalex.org/keywords/diatomic-molecule","display_name":"Diatomic molecule","score":0.5671290755271912},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.5500820279121399},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.5392592549324036},{"id":"https://openalex.org/keywords/classical-mechanics","display_name":"Classical mechanics","score":0.5179023742675781},{"id":"https://openalex.org/keywords/potential-energy","display_name":"Potential energy","score":0.4657128155231476},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.45881256461143494},{"id":"https://openalex.org/keywords/cube","display_name":"Cube (algebra)","score":0.4351205825805664},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.23369047045707703},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.21168500185012817},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.11200442910194397}],"concepts":[{"id":"https://openalex.org/C208081375","wikidata":"https://www.wikidata.org/wiki/Q274502","display_name":"Degrees of freedom (physics and chemistry)","level":2,"score":0.7733912467956543},{"id":"https://openalex.org/C135889238","wikidata":"https://www.wikidata.org/wiki/Q46276","display_name":"Kinetic energy","level":2,"score":0.7682518362998962},{"id":"https://openalex.org/C99742106","wikidata":"https://www.wikidata.org/wiki/Q255996","display_name":"Equipartition theorem","level":3,"score":0.7526895403862},{"id":"https://openalex.org/C111806078","wikidata":"https://www.wikidata.org/wiki/Q1751859","display_name":"Diatomic molecule","level":3,"score":0.5671290755271912},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.5500820279121399},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.5392592549324036},{"id":"https://openalex.org/C74650414","wikidata":"https://www.wikidata.org/wiki/Q11397","display_name":"Classical mechanics","level":1,"score":0.5179023742675781},{"id":"https://openalex.org/C84551667","wikidata":"https://www.wikidata.org/wiki/Q155640","display_name":"Potential energy","level":2,"score":0.4657128155231476},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.45881256461143494},{"id":"https://openalex.org/C53051483","wikidata":"https://www.wikidata.org/wiki/Q861555","display_name":"Cube (algebra)","level":2,"score":0.4351205825805664},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.23369047045707703},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.21168500185012817},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.11200442910194397},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.0},{"id":"https://openalex.org/C115260700","wikidata":"https://www.wikidata.org/wiki/Q11408","display_name":"Magnetic field","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1002/(sici)1096-987x(199805)19:7<726::aid-jcc4>3.0.co;2-s","is_oa":false,"landing_page_url":"https://doi.org/10.1002/(sici)1096-987x(199805)19:7<726::aid-jcc4>3.0.co;2-s","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"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/16","score":0.6200000047683716,"display_name":"Peace, Justice and strong institutions"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W1595169993","https://openalex.org/W1970747580","https://openalex.org/W1971820073","https://openalex.org/W1975945758","https://openalex.org/W1992587635","https://openalex.org/W1993227183","https://openalex.org/W1997629201","https://openalex.org/W2002677634","https://openalex.org/W2017835622","https://openalex.org/W2035266068","https://openalex.org/W2038610243","https://openalex.org/W2043610432","https://openalex.org/W2048833115","https://openalex.org/W2052638779","https://openalex.org/W2054372370","https://openalex.org/W2056208263","https://openalex.org/W2067964076","https://openalex.org/W2084367325","https://openalex.org/W2124555222","https://openalex.org/W2138199172","https://openalex.org/W2146462263","https://openalex.org/W2159795585","https://openalex.org/W2162721376","https://openalex.org/W2323178299","https://openalex.org/W2905826917","https://openalex.org/W4230191709","https://openalex.org/W4299790875"],"related_works":["https://openalex.org/W2087867901","https://openalex.org/W2151201349","https://openalex.org/W2040139964","https://openalex.org/W2009267045","https://openalex.org/W2052844936","https://openalex.org/W2187980052","https://openalex.org/W2044479874","https://openalex.org/W2078274232","https://openalex.org/W2089555233","https://openalex.org/W2054323387"],"abstract_inverted_index":{"This":[0],"article":[1],"describes":[2],"an":[3,159],"unexpected":[4],"phenomenon":[5,120],"encountered":[6],"during":[7],"MD":[8,155],"simulations:":[9],"velocity":[10],"rescaling":[11],"using":[12,180],"standard":[13],"protocols":[14],"can":[15],"systematically":[16],"change":[17],"the":[18,30,38,41,74,81,91,112,142,145,178,193,208],"proportion":[19],"of":[20,33,43,45,53,58,64,77,83,90,100,115,130,138,144,154,173],"total":[21],"kinetic":[22,51,92,108],"energy":[23,52,93,109],"(KE)":[24],"found":[25],"in":[26,55,160,175],"motions":[27],"associated":[28,110],"with":[29,105,111,135,186],"various":[31],"degrees":[32,114,137],"freedom.":[34,59,116],"Under":[35],"these":[36,97],"conditions,":[37,191],"simulation":[39,162],"violates":[40],"principle":[42],"equipartition":[44],"energy,":[46],"which":[47],"requires":[48],"a":[49,103,127,131,164,169,181],"mean":[50],"RT/2":[54],"each":[56],"degree":[57],"A":[60],"particularly":[61],"pathological":[62],"form":[63],"this":[65,86,119],"problem":[66],"occurs":[67],"if":[68],"one":[69,157,167],"does":[70],"not":[71],"periodically":[72],"remove":[73],"net":[75],"translation":[76],"(and":[78],"rotation":[79],"about)":[80],"center":[82],"mass.":[84],"In":[85],"case,":[87],"almost":[88,106],"all":[89],"is":[94],"converted":[95],"into":[96],"two":[98,136],"kinds":[99,153],"motion,":[101],"producing":[102],"system":[104,134],"no":[107],"internal":[113],"We":[117,125,147],"call":[118],"\u201cthe":[121],"flying":[122],"ice":[123],"cube.\u201d":[124],"present":[126,149],"mathematical":[128],"analysis":[129],"simple":[132],"diatomic":[133,165],"freedom,":[139],"to":[140],"document":[141],"origin":[143],"problem.":[146,209],"then":[148],"examples":[150],"from":[151],"three":[152],"simulations,":[156],"being":[158],"vacuo":[161],"on":[163],"system,":[166],"involving":[168],"low":[170],"resolution":[171],"model":[172,185],"DNA":[174,184],"vacuo,":[176],"and":[177,192],"third":[179],"traditional":[182],"all-atom":[183],"full":[187],"solvation,":[188],"periodic":[189],"boundary":[190],"particle":[194],"mesh":[195],"Ewald":[196],"method":[197],"for":[198,206],"treating":[199],"long-range":[200],"electrostatics.":[201],"Finally,":[202],"we":[203],"discuss":[204],"methods":[205],"avoiding":[207],"\u00a9":[210],"1998":[211,222],"John":[212],"Wiley":[213],"&":[214],"Sons,":[215],"Inc.":[216],"J":[217],"Comput":[218],"Chem":[219],"19:":[220],"726\u2013740,":[221]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":14},{"year":2022,"cited_by_count":10},{"year":2021,"cited_by_count":19},{"year":2020,"cited_by_count":15},{"year":2019,"cited_by_count":10},{"year":2018,"cited_by_count":15},{"year":2017,"cited_by_count":39},{"year":2016,"cited_by_count":20},{"year":2015,"cited_by_count":22},{"year":2014,"cited_by_count":21},{"year":2013,"cited_by_count":14},{"year":2012,"cited_by_count":23}],"updated_date":"2026-03-15T09:29:46.208133","created_date":"2025-10-10T00:00:00"}