{"id":"https://openalex.org/W2154613309","doi":"https://doi.org/10.1002/jcc.10243","title":"nMoldyn: A program package for a neutron scattering oriented analysis of molecular dynamics simulations","display_name":"nMoldyn: A program package for a neutron scattering oriented analysis of molecular dynamics simulations","publication_year":2003,"publication_date":"2003-03-05","ids":{"openalex":"https://openalex.org/W2154613309","doi":"https://doi.org/10.1002/jcc.10243","mag":"2154613309","pmid":"https://pubmed.ncbi.nlm.nih.gov/12632481"},"language":"en","primary_location":{"id":"doi:10.1002/jcc.10243","is_oa":false,"landing_page_url":"https://doi.org/10.1002/jcc.10243","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/A5029212835","display_name":"Tomasz R\u00f3g","orcid":"https://orcid.org/0000-0001-6765-7013"},"institutions":[{"id":"https://openalex.org/I126596746","display_name":"Jagiellonian University","ror":"https://ror.org/03bqmcz70","country_code":"PL","type":"education","lineage":["https://openalex.org/I126596746"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210118525","display_name":"Centre de Biophysique Mol\u00e9culaire","ror":"https://ror.org/02dpqcy73","country_code":"FR","type":"facility","lineage":["https://openalex.org/I110017253","https://openalex.org/I12449238","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I4210096427","https://openalex.org/I4210118525","https://openalex.org/I4210128300"]}],"countries":["FR","PL"],"is_corresponding":false,"raw_author_name":"T. R\u00f3g","raw_affiliation_strings":["Departament of Biophysics, Institute of Molecular Biology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Krak\u00f3w, Poland","Centre de Biophysique Mole\u0301culaire (UPR 4301 CNRS), Rue Charles Sadron, 45071 Orle\u0301ans Cedex 2, France","Departament of Biophysics, Institute of Molecular Biology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Krako\u0301w, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departament of Biophysics, Institute of Molecular Biology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Krak\u00f3w, Poland","institution_ids":["https://openalex.org/I126596746"]},{"raw_affiliation_string":"Centre de Biophysique Mole\u0301culaire (UPR 4301 CNRS), Rue Charles Sadron, 45071 Orle\u0301ans Cedex 2, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210118525"]},{"raw_affiliation_string":"Departament of Biophysics, Institute of Molecular Biology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Krako\u0301w, Poland","institution_ids":["https://openalex.org/I126596746"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042434773","display_name":"Krzysztof Murzyn","orcid":"https://orcid.org/0000-0002-7064-9900"},"institutions":[{"id":"https://openalex.org/I126596746","display_name":"Jagiellonian University","ror":"https://ror.org/03bqmcz70","country_code":"PL","type":"education","lineage":["https://openalex.org/I126596746"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210118525","display_name":"Centre de Biophysique Mol\u00e9culaire","ror":"https://ror.org/02dpqcy73","country_code":"FR","type":"facility","lineage":["https://openalex.org/I110017253","https://openalex.org/I12449238","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I4210096427","https://openalex.org/I4210118525","https://openalex.org/I4210128300"]}],"countries":["FR","PL"],"is_corresponding":false,"raw_author_name":"K. Murzyn","raw_affiliation_strings":["Centre de Biophysique Mole\u0301culaire (UPR 4301 CNRS), Rue Charles Sadron, 45071 Orle\u0301ans Cedex 2, France","Departament of Biophysics, Institute of Molecular Biology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Krako\u0301w, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre de Biophysique Mole\u0301culaire (UPR 4301 CNRS), Rue Charles Sadron, 45071 Orle\u0301ans Cedex 2, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210118525"]},{"raw_affiliation_string":"Departament of Biophysics, Institute of Molecular Biology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Krako\u0301w, Poland","institution_ids":["https://openalex.org/I126596746"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008543195","display_name":"Konrad Hinsen","orcid":"https://orcid.org/0000-0003-0330-9428"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210118525","display_name":"Centre de Biophysique Mol\u00e9culaire","ror":"https://ror.org/02dpqcy73","country_code":"FR","type":"facility","lineage":["https://openalex.org/I110017253","https://openalex.org/I12449238","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I4210096427","https://openalex.org/I4210118525","https://openalex.org/I4210128300"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"K. Hinsen","raw_affiliation_strings":["Centre de Biophysique Mole\u0301culaire (UPR 4301 CNRS), Rue Charles Sadron, 45071 Orle\u0301ans Cedex 2, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre de Biophysique Mole\u0301culaire (UPR 4301 CNRS), Rue Charles Sadron, 45071 Orle\u0301ans Cedex 2, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210118525"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5038965944","display_name":"Gerald R. Kneller","orcid":"https://orcid.org/0000-0002-3374-3797"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210118525","display_name":"Centre de Biophysique Mol\u00e9culaire","ror":"https://ror.org/02dpqcy73","country_code":"FR","type":"facility","lineage":["https://openalex.org/I110017253","https://openalex.org/I12449238","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I4210096427","https://openalex.org/I4210118525","https://openalex.org/I4210128300"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"G. R. Kneller","raw_affiliation_strings":["Centre de Biophysique Mole\u0301culaire (UPR 4301 CNRS), Rue Charles Sadron, 45071 Orle\u0301ans Cedex 2, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre de Biophysique Mole\u0301culaire (UPR 4301 CNRS), Rue Charles Sadron, 45071 Orle\u0301ans Cedex 2, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210118525"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5038965944"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210118525"],"apc_list":{"value":4520,"currency":"USD","value_usd":4520},"apc_paid":null,"fwci":6.0346,"has_fulltext":false,"cited_by_count":199,"citation_normalized_percentile":{"value":0.96992008,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":100},"biblio":{"volume":"24","issue":"5","first_page":"657","last_page":"667"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10413","display_name":"High-pressure geophysics and materials","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1908","display_name":"Geophysics"},"field":{"id":"https://openalex.org/fields/19","display_name":"Earth and Planetary Sciences"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10413","display_name":"High-pressure geophysics and materials","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1908","display_name":"Geophysics"},"field":{"id":"https://openalex.org/fields/19","display_name":"Earth and Planetary Sciences"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11809","display_name":"Advanced NMR Techniques and Applications","score":0.9986000061035156,"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"}},{"id":"https://openalex.org/T11949","display_name":"Nuclear Physics and Applications","score":0.9984999895095825,"subfield":{"id":"https://openalex.org/subfields/3108","display_name":"Radiation"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/autocorrelation","display_name":"Autocorrelation","score":0.7378619313240051},{"id":"https://openalex.org/keywords/fourier-transform","display_name":"Fourier transform","score":0.6783036589622498},{"id":"https://openalex.org/keywords/neutron-scattering","display_name":"Neutron scattering","score":0.5408523678779602},{"id":"https://openalex.org/keywords/fast-fourier-transform","display_name":"Fast Fourier transform","score":0.4777199923992157},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.4728313386440277},{"id":"https://openalex.org/keywords/scattering","display_name":"Scattering","score":0.4622715413570404},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.4401945173740387},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.43565860390663147},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.42787569761276245},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.39937737584114075},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.39669269323349},{"id":"https://openalex.org/keywords/computational-physics","display_name":"Computational physics","score":0.37720680236816406},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.34191977977752686},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.2770269513130188},{"id":"https://openalex.org/keywords/optics","display_name":"Optics","score":0.2666141986846924},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2295016646385193},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.18715208768844604}],"concepts":[{"id":"https://openalex.org/C5297727","wikidata":"https://www.wikidata.org/wiki/Q786970","display_name":"Autocorrelation","level":2,"score":0.7378619313240051},{"id":"https://openalex.org/C102519508","wikidata":"https://www.wikidata.org/wiki/Q6520159","display_name":"Fourier transform","level":2,"score":0.6783036589622498},{"id":"https://openalex.org/C104015590","wikidata":"https://www.wikidata.org/wiki/Q1451740","display_name":"Neutron scattering","level":3,"score":0.5408523678779602},{"id":"https://openalex.org/C75172450","wikidata":"https://www.wikidata.org/wiki/Q623950","display_name":"Fast Fourier transform","level":2,"score":0.4777199923992157},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4728313386440277},{"id":"https://openalex.org/C191486275","wikidata":"https://www.wikidata.org/wiki/Q210028","display_name":"Scattering","level":2,"score":0.4622715413570404},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.4401945173740387},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.43565860390663147},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.42787569761276245},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.39937737584114075},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.39669269323349},{"id":"https://openalex.org/C30475298","wikidata":"https://www.wikidata.org/wiki/Q909554","display_name":"Computational physics","level":1,"score":0.37720680236816406},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.34191977977752686},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2770269513130188},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.2666141986846924},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2295016646385193},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.18715208768844604},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1002/jcc.10243","is_oa":false,"landing_page_url":"https://doi.org/10.1002/jcc.10243","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:12632481","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/12632481","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":"Journal Article"},{"id":"pmh:oai:HAL:hal-02154080v1","is_oa":false,"landing_page_url":"https://hal.science/hal-02154080","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Computational Chemistry, 2003, 24 (5), pp.657-667. ⟨10.1002/jcc.10243⟩","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":37,"referenced_works":["https://openalex.org/W275680155","https://openalex.org/W634059855","https://openalex.org/W1496923911","https://openalex.org/W1527895848","https://openalex.org/W1569297620","https://openalex.org/W1583065847","https://openalex.org/W1585382007","https://openalex.org/W1966264494","https://openalex.org/W1967131642","https://openalex.org/W1980450508","https://openalex.org/W2010793745","https://openalex.org/W2014154953","https://openalex.org/W2015761349","https://openalex.org/W2021885941","https://openalex.org/W2029025693","https://openalex.org/W2039457516","https://openalex.org/W2041902442","https://openalex.org/W2054740881","https://openalex.org/W2059268749","https://openalex.org/W2081440105","https://openalex.org/W2104536090","https://openalex.org/W2138871907","https://openalex.org/W2143981766","https://openalex.org/W2151047202","https://openalex.org/W2158528359","https://openalex.org/W2164607721","https://openalex.org/W2341283081","https://openalex.org/W2468249787","https://openalex.org/W2569817081","https://openalex.org/W3003567061","https://openalex.org/W3016843226","https://openalex.org/W3022893215","https://openalex.org/W4230880638","https://openalex.org/W4237491802","https://openalex.org/W4285719527","https://openalex.org/W4301253858","https://openalex.org/W4301623764"],"related_works":["https://openalex.org/W2341492732","https://openalex.org/W3187193180","https://openalex.org/W106542691","https://openalex.org/W4287027380","https://openalex.org/W1699080303","https://openalex.org/W4297799326","https://openalex.org/W3116064965","https://openalex.org/W3193760048","https://openalex.org/W747394405","https://openalex.org/W1486009489"],"abstract_inverted_index":{"We":[0],"present":[1],"a":[2,43,58,74,166],"new":[3,33,63,167],"implementation":[4,34],"of":[5,18,38,73,79,108,148],"the":[6,14,36,39,71,93,96,114,123,134,145,149,154],"program":[7],"nMoldyn,":[8],"which":[9],"has":[10],"been":[11],"developed":[12],"for":[13,61],"computation":[15],"and":[16,51,53,78,110,119,127,136,153,168],"decomposition":[17],"neutron":[19,132],"scattering":[20,139,151],"intensities":[21],"from":[22],"Molecular":[23],"Dynamics":[24],"trajectories":[25],"(Comp.":[26],"Phys.":[27],"Commun":[28],"1995,":[29],"91,":[30],"191-214).":[31],"The":[32,84,159],"extends":[35],"functionality":[37],"original":[40],"version,":[41],"provides":[42],"much":[44],"more":[45],"convenient":[46],"user":[47],"interface":[48],"(both":[49],"graphical/interactive":[50],"batch),":[52],"can":[54,87],"be":[55,88],"used":[56],"as":[57,100,102],"tool":[59],"set":[60],"implementing":[62],"analysis":[64],"modules.":[65],"This":[66],"was":[67],"made":[68],"possible":[69],"by":[70,90],"use":[72],"high-level":[75],"language,":[76],"Python,":[77],"modern":[80],"object-oriented":[81],"programming":[82],"techniques.":[83],"quantities":[85],"that":[86,171],"calculated":[89],"nMoldyn":[91],"are":[92],"mean-square":[94],"displacement,":[95],"velocity":[97,116],"autocorrelation":[98,117],"function":[99,118,147,164],"well":[101],"its":[103,111,120],"Fourier":[104,121,143],"transform":[105],"(the":[106],"density":[107],"states)":[109],"memory":[112,146,163],"function,":[113,126,152],"angular":[115],"transform,":[122],"reorientational":[124],"correlation":[125],"several":[128],"functions":[129,140],"specific":[130],"to":[131,161,173,177],"scattering:":[133],"coherent":[135,150],"incoherent":[137,156],"intermediate":[138],"with":[141],"their":[142],"transforms,":[144],"elastic":[155],"structure":[157],"factor.":[158],"possibility":[160],"compute":[162],"is":[165],"powerful":[169],"feature":[170],"allows":[172],"relate":[174],"simulation":[175],"results":[176],"theoretical":[178],"studies.":[179]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":11},{"year":2017,"cited_by_count":10},{"year":2016,"cited_by_count":12},{"year":2015,"cited_by_count":9},{"year":2014,"cited_by_count":15},{"year":2013,"cited_by_count":15},{"year":2012,"cited_by_count":14}],"updated_date":"2026-09-11T09:22:31.653822","created_date":"2016-06-24T00:00:00"}