{"id":"https://openalex.org/W2963325382","doi":"https://doi.org/10.25080/majora-7ddc1dd1-013","title":"PMDA - Parallel Molecular Dynamics Analysis","display_name":"PMDA - Parallel Molecular Dynamics Analysis","publication_year":2019,"publication_date":"2019-01-01","ids":{"openalex":"https://openalex.org/W2963325382","doi":"https://doi.org/10.25080/majora-7ddc1dd1-013","mag":"2963325382"},"language":"en","primary_location":{"id":"doi:10.25080/majora-7ddc1dd1-013","is_oa":true,"landing_page_url":"https://doi.org/10.25080/majora-7ddc1dd1-013","pdf_url":"http://conference.scipy.org/proceedings/scipy2019/pdfs/shujie_fan.pdf","source":{"id":"https://openalex.org/S4220651651","display_name":"Proceedings of the Python in Science Conferences","issn_l":"2575-9752","issn":["2575-9752"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the Python in Science Conference","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"http://conference.scipy.org/proceedings/scipy2019/pdfs/shujie_fan.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5079003974","display_name":"Shujie Fan","orcid":"https://orcid.org/0000-0002-0271-2760"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Shujie Fan","raw_affiliation_strings":["Arizona State University || Max Planck Institute of Biophysics *"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Arizona State University || Max Planck Institute of Biophysics *","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071215879","display_name":"Max Linke","orcid":"https://orcid.org/0000-0002-7208-5088"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Max Linke","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026015850","display_name":"Ioannis Paraskevakos","orcid":null},"institutions":[{"id":"https://openalex.org/I4210096112","display_name":"Rutgers Sexual and Reproductive Health and Rights","ror":"https://ror.org/00rcvgx40","country_code":"NL","type":"other","lineage":["https://openalex.org/I4210096112"]},{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]},{"id":"https://openalex.org/I179093154","display_name":"University of New Hampshire at Manchester","ror":"https://ror.org/04pvpk743","country_code":"US","type":"education","lineage":["https://openalex.org/I179093154"]},{"id":"https://openalex.org/I161057412","display_name":"University of New Hampshire","ror":"https://ror.org/01rmh9n78","country_code":"US","type":"education","lineage":["https://openalex.org/I161057412"]}],"countries":["NL","US"],"is_corresponding":false,"raw_author_name":"Ioannis Paraskevakos","raw_affiliation_strings":["Rutgers University  University of New Hampshire","Rutgers University \u2021 University of New Hampshire"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Rutgers University  University of New Hampshire","institution_ids":["https://openalex.org/I4210096112","https://openalex.org/I102322142"]},{"raw_affiliation_string":"Rutgers University \u2021 University of New Hampshire","institution_ids":["https://openalex.org/I161057412","https://openalex.org/I179093154","https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067172880","display_name":"Richard Gowers","orcid":"https://orcid.org/0000-0002-3241-1846"},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]},{"id":"https://openalex.org/I4210096112","display_name":"Rutgers Sexual and Reproductive Health and Rights","ror":"https://ror.org/00rcvgx40","country_code":"NL","type":"other","lineage":["https://openalex.org/I4210096112"]},{"id":"https://openalex.org/I179093154","display_name":"University of New Hampshire at Manchester","ror":"https://ror.org/04pvpk743","country_code":"US","type":"education","lineage":["https://openalex.org/I179093154"]},{"id":"https://openalex.org/I161057412","display_name":"University of New Hampshire","ror":"https://ror.org/01rmh9n78","country_code":"US","type":"education","lineage":["https://openalex.org/I161057412"]}],"countries":["NL","US"],"is_corresponding":false,"raw_author_name":"Richard Gowers","raw_affiliation_strings":["Rutgers University  University of New Hampshire","Rutgers University \u2021 University of New Hampshire"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Rutgers University  University of New Hampshire","institution_ids":["https://openalex.org/I4210096112","https://openalex.org/I102322142"]},{"raw_affiliation_string":"Rutgers University \u2021 University of New Hampshire","institution_ids":["https://openalex.org/I161057412","https://openalex.org/I179093154","https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033219019","display_name":"Michael Gecht","orcid":"https://orcid.org/0000-0002-4643-6593"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Michael Gecht","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5028356492","display_name":"Oliver Beckstein","orcid":"https://orcid.org/0000-0003-1340-0831"},"institutions":[{"id":"https://openalex.org/I179093154","display_name":"University of New Hampshire at Manchester","ror":"https://ror.org/04pvpk743","country_code":"US","type":"education","lineage":["https://openalex.org/I179093154"]},{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]},{"id":"https://openalex.org/I4210096112","display_name":"Rutgers Sexual and Reproductive Health and Rights","ror":"https://ror.org/00rcvgx40","country_code":"NL","type":"other","lineage":["https://openalex.org/I4210096112"]},{"id":"https://openalex.org/I161057412","display_name":"University of New Hampshire","ror":"https://ror.org/01rmh9n78","country_code":"US","type":"education","lineage":["https://openalex.org/I161057412"]}],"countries":["NL","US"],"is_corresponding":true,"raw_author_name":"Oliver Beckstein","raw_affiliation_strings":["Arizona State University || Max Planck Institute of Biophysics *","Rutgers University  University of New Hampshire","Rutgers University \u2021 University of New Hampshire"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Arizona State University || Max Planck Institute of Biophysics *","institution_ids":[]},{"raw_affiliation_string":"Rutgers University  University of New Hampshire","institution_ids":["https://openalex.org/I4210096112","https://openalex.org/I102322142"]},{"raw_affiliation_string":"Rutgers University \u2021 University of New Hampshire","institution_ids":["https://openalex.org/I161057412","https://openalex.org/I179093154","https://openalex.org/I102322142"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5028356492"],"corresponding_institution_ids":["https://openalex.org/I102322142","https://openalex.org/I161057412","https://openalex.org/I179093154","https://openalex.org/I4210096112"],"apc_list":null,"apc_paid":null,"fwci":1.2373,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":{"value":0.75996216,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":null,"issue":null,"first_page":"134","last_page":"142"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.9923999905586243,"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"}},"topics":[{"id":"https://openalex.org/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.9923999905586243,"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/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.9918000102043152,"subfield":{"id":"https://openalex.org/subfields/1708","display_name":"Hardware and Architecture"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9912999868392944,"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/computer-science","display_name":"Computer science","score":0.8566781878471375},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.653633177280426},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.6460557579994202},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.5769631266593933},{"id":"https://openalex.org/keywords/laptop","display_name":"Laptop","score":0.5762336850166321},{"id":"https://openalex.org/keywords/block","display_name":"Block (permutation group theory)","score":0.4775713086128235},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.4757796823978424},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.428469717502594},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.2797541320323944}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8566781878471375},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.653633177280426},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.6460557579994202},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.5769631266593933},{"id":"https://openalex.org/C2780008327","wikidata":"https://www.wikidata.org/wiki/Q3962","display_name":"Laptop","level":2,"score":0.5762336850166321},{"id":"https://openalex.org/C2777210771","wikidata":"https://www.wikidata.org/wiki/Q4927124","display_name":"Block (permutation group theory)","level":2,"score":0.4775713086128235},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.4757796823978424},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.428469717502594},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.2797541320323944},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.25080/majora-7ddc1dd1-013","is_oa":true,"landing_page_url":"https://doi.org/10.25080/majora-7ddc1dd1-013","pdf_url":"http://conference.scipy.org/proceedings/scipy2019/pdfs/shujie_fan.pdf","source":{"id":"https://openalex.org/S4220651651","display_name":"Proceedings of the Python in Science Conferences","issn_l":"2575-9752","issn":["2575-9752"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the Python in Science Conference","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.25080/majora-7ddc1dd1-013","is_oa":true,"landing_page_url":"https://doi.org/10.25080/majora-7ddc1dd1-013","pdf_url":"http://conference.scipy.org/proceedings/scipy2019/pdfs/shujie_fan.pdf","source":{"id":"https://openalex.org/S4220651651","display_name":"Proceedings of the Python in Science Conferences","issn_l":"2575-9752","issn":["2575-9752"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the Python in Science Conference","raw_type":"proceedings-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.4699999988079071}],"awards":[{"id":"https://openalex.org/G367708065","display_name":null,"funder_award_id":"ACI-1548562","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3709464396","display_name":null,"funder_award_id":"-1548562","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3730782400","display_name":"XSEDE 2.0:  Integrating, Enabling and Enhancing National Cyberinfrastructure with Expanding Community Involvement","funder_award_id":"1548562","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4716253616","display_name":"CIF21 DIBBs: Middleware and High Performance Analytics Libraries for Scalable Data Science","funder_award_id":"1443054","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4897854425","display_name":null,"funder_award_id":"grant number ACI-1548562","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320316545","display_name":"San Diego Supercomputer Center","ror":"https://ror.org/04mg3nk07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2963325382.pdf","grobid_xml":"https://content.openalex.org/works/W2963325382.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W1162436746","https://openalex.org/W1507573241","https://openalex.org/W1548618691","https://openalex.org/W1964718104","https://openalex.org/W1966127665","https://openalex.org/W1979566015","https://openalex.org/W1979847955","https://openalex.org/W2005263403","https://openalex.org/W2021769046","https://openalex.org/W2043701535","https://openalex.org/W2093221728","https://openalex.org/W2110114082","https://openalex.org/W2121400889","https://openalex.org/W2122576346","https://openalex.org/W2140628770","https://openalex.org/W2146292423","https://openalex.org/W2150871235","https://openalex.org/W2152238488","https://openalex.org/W2154449781","https://openalex.org/W2170711116","https://openalex.org/W2510475640","https://openalex.org/W2527672088","https://openalex.org/W2751229375","https://openalex.org/W2793998831","https://openalex.org/W2801084441","https://openalex.org/W2807275545","https://openalex.org/W2883596424","https://openalex.org/W2885483166","https://openalex.org/W2892745578","https://openalex.org/W2902069072","https://openalex.org/W2963179050","https://openalex.org/W2968171084","https://openalex.org/W3100104164","https://openalex.org/W4288400169"],"related_works":["https://openalex.org/W2119821807","https://openalex.org/W1509211761","https://openalex.org/W2391299576","https://openalex.org/W1588481459","https://openalex.org/W2011313916","https://openalex.org/W3150687539","https://openalex.org/W2133693067","https://openalex.org/W1531488649","https://openalex.org/W1585350690","https://openalex.org/W2366027386"],"abstract_inverted_index":{"MDAnalysis":[0,81,93],"is":[1,38,52,114,119,243],"an":[2],"object-oriented":[3],"Python":[4,76],"library":[5,77],"to":[6,41,82,141,161,231,235,252,255],"analyze":[7],"trajectories":[8,37],"from":[9,131,233,249],"molecular":[10,260],"dynamics":[11,261],"(MD)":[12],"simulations":[13],"in":[14,44,92,123,171,178,239],"many":[15,42],"popular":[16],"formats.":[17],"With":[18],"the":[19,33,70,99,196,216,224],"development":[20],"of":[21,35,49,198,218,259],"highly":[22],"optimized":[23],"MD":[24],"software":[25],"packages":[26],"on":[27,125,182,200,206,223,246],"high":[28],"performance":[29,197,217],"computing":[30],"(HPC)":[31],"resources,":[32],"size":[34],"simulation":[36],"growing":[39],"up":[40,257],"terabytes":[43],"size.":[45],"However":[46],"efficient":[47],"usage":[48],"multicore":[50],"architecture":[51],"a":[53,62,75,95,104,154,179,187,192,207],"challenge":[54],"for":[55,65,108],"MDAnalysis,":[56],"which":[57],"does":[58],"not":[59],"yet":[60],"provide":[61,83],"standard":[63],"interface":[64,156],"parallel":[66,84,109,124,143,164],"analysis.":[67,111],"To":[68],"address":[69],"challenge,":[71],"we":[72],"developed":[73],"PMDA,":[74],"that":[78,157,213],"builds":[79],"upon":[80],"analysis":[85,90,118,145,148,165,177,220,225,258],"algorithms.":[86],"PMDA":[87,138,167,199],"parallelizes":[88],"common":[89,155],"algorithms":[91],"through":[94],"task-based":[96],"approach":[97],"with":[98,146],"Dask":[100],"library.":[101],"We":[102,194],"implement":[103],"simple":[105],"split-apply-combine":[106],"scheme":[107],"trajectory":[110,113,144,219],"The":[112,210],"split":[115],"into":[116],"blocks,":[117],"performed":[120],"separately":[121],"and":[122,136,173,203],"each":[126,132],"block":[127,133],"(\"apply\"),":[128],"then":[129],"results":[130,211],"are":[134],"gathered":[135],"combined.":[137],"allows":[139],"one":[140,174],"perform":[142],"pre-defined":[147],"tasks.":[149],"In":[150],"addition,":[151],"it":[152,159,242],"provides":[153],"makes":[158],"easy":[160],"create":[162],"user-defined":[163],"modules.":[166],"supports":[168],"all":[169],"schedulers":[170],"Dask,":[172],"can":[175,227],"run":[176],"distributed":[180],"fashion":[181],"HPC":[183],"machines,":[184],"ad-hoc":[185],"clusters,":[186],"single":[188,201],"multi-core":[189,250],"workstation":[190],"or":[191],"laptop.":[193],"tested":[195],"node":[202],"multiple":[204],"nodes":[205],"national":[208],"supercomputer.":[209],"show":[212],"parallelization":[214],"improves":[215],"and,":[221],"depending":[222],"task,":[226],"cut":[228],"down":[229],"time":[230],"solution":[232],"hours":[234],"minutes.":[236],"Although":[237],"still":[238],"alpha":[240],"stage,":[241],"already":[244],"used":[245],"resources":[247],"ranging":[248],"laptops":[251],"XSEDE":[253],"supercomputers":[254],"speed":[256],"trajectories.":[262]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":3}],"updated_date":"2026-06-22T08:00:12.763002","created_date":"2025-10-10T00:00:00"}
