{"id":"https://openalex.org/W4408347666","doi":"https://doi.org/10.1016/j.softx.2025.102118","title":"Gromologist: A GROMACS-oriented utility library for structure and topology manipulation","display_name":"Gromologist: A GROMACS-oriented utility library for structure and topology manipulation","publication_year":2025,"publication_date":"2025-03-12","ids":{"openalex":"https://openalex.org/W4408347666","doi":"https://doi.org/10.1016/j.softx.2025.102118"},"language":"en","primary_location":{"id":"doi:10.1016/j.softx.2025.102118","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.softx.2025.102118","pdf_url":null,"source":{"id":"https://openalex.org/S2506067282","display_name":"SoftwareX","issn_l":"2352-7110","issn":["2352-7110"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"SoftwareX","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1016/j.softx.2025.102118","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5085108119","display_name":"Mi\u0142osz Wiecz\u00f3r","orcid":"https://orcid.org/0000-0003-4990-8629"},"institutions":[{"id":"https://openalex.org/I169333911","display_name":"Gda\u0144sk University of Technology","ror":"https://ror.org/006x4sc24","country_code":"PL","type":"education","lineage":["https://openalex.org/I169333911"]},{"id":"https://openalex.org/I40413290","display_name":"University of Gda\u0144sk","ror":"https://ror.org/011dv8m48","country_code":"PL","type":"education","lineage":["https://openalex.org/I40413290"]},{"id":"https://openalex.org/I4210122345","display_name":"Institute for Research in Biomedicine","ror":"https://ror.org/01z1gye03","country_code":"ES","type":"healthcare","lineage":["https://openalex.org/I4210122345","https://openalex.org/I4210132884","https://openalex.org/I4387153040"]}],"countries":["ES","PL"],"is_corresponding":true,"raw_author_name":"Mi\u0142osz Wiecz\u00f3r","raw_affiliation_strings":["Department of Physical Chemistry, Gda\u0144sk University of Technology, Poland","Molecular Modeling and Bioinformatics, IRB Barcelona, Spain"],"raw_orcid":"https://orcid.org/0000-0003-4990-8629","affiliations":[{"raw_affiliation_string":"Department of Physical Chemistry, Gda\u0144sk University of Technology, Poland","institution_ids":["https://openalex.org/I169333911","https://openalex.org/I40413290"]},{"raw_affiliation_string":"Molecular Modeling and Bioinformatics, IRB Barcelona, Spain","institution_ids":["https://openalex.org/I4210122345"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050111942","display_name":"Jacek Czub","orcid":"https://orcid.org/0000-0003-3639-6935"},"institutions":[{"id":"https://openalex.org/I169333911","display_name":"Gda\u0144sk University of Technology","ror":"https://ror.org/006x4sc24","country_code":"PL","type":"education","lineage":["https://openalex.org/I169333911"]},{"id":"https://openalex.org/I40413290","display_name":"University of Gda\u0144sk","ror":"https://ror.org/011dv8m48","country_code":"PL","type":"education","lineage":["https://openalex.org/I40413290"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Jacek Czub","raw_affiliation_strings":["Department of Physical Chemistry, Gda\u0144sk University of Technology, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physical Chemistry, Gda\u0144sk University of Technology, Poland","institution_ids":["https://openalex.org/I169333911","https://openalex.org/I40413290"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006399866","display_name":"Modesto Orozco","orcid":"https://orcid.org/0000-0002-8608-3278"},"institutions":[{"id":"https://openalex.org/I4210122345","display_name":"Institute for Research in Biomedicine","ror":"https://ror.org/01z1gye03","country_code":"ES","type":"healthcare","lineage":["https://openalex.org/I4210122345","https://openalex.org/I4210132884","https://openalex.org/I4387153040"]},{"id":"https://openalex.org/I71999127","display_name":"Universitat de Barcelona","ror":"https://ror.org/021018s57","country_code":"ES","type":"education","lineage":["https://openalex.org/I71999127"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Modesto Orozco","raw_affiliation_strings":["Faculty of Biology, University of Barcelona, Spain","Molecular Modeling and Bioinformatics, IRB Barcelona, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Biology, University of Barcelona, Spain","institution_ids":["https://openalex.org/I71999127"]},{"raw_affiliation_string":"Molecular Modeling and Bioinformatics, IRB Barcelona, Spain","institution_ids":["https://openalex.org/I4210122345"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5085108119"],"corresponding_institution_ids":["https://openalex.org/I169333911","https://openalex.org/I40413290","https://openalex.org/I4210122345"],"apc_list":{"value":500,"currency":"USD","value_usd":500},"apc_paid":{"value":500,"currency":"USD","value_usd":500},"fwci":8.3548,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.97312641,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"30","issue":null,"first_page":"102118","last_page":"102118"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.9772999882698059,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.9772999882698059,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"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/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.9768999814987183,"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/T10923","display_name":"Force Microscopy Techniques and Applications","score":0.925599992275238,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.740161657333374},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.444827139377594},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.37900394201278687},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.34455522894859314},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.3271191716194153},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.3252067565917969},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.32510215044021606},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.11962622404098511},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.10181465744972229}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.740161657333374},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.444827139377594},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.37900394201278687},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.34455522894859314},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.3271191716194153},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.3252067565917969},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.32510215044021606},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.11962622404098511},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.10181465744972229}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1016/j.softx.2025.102118","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.softx.2025.102118","pdf_url":null,"source":{"id":"https://openalex.org/S2506067282","display_name":"SoftwareX","issn_l":"2352-7110","issn":["2352-7110"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"SoftwareX","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:01782f13c138428bbb6e70260370c042","is_oa":true,"landing_page_url":"https://doaj.org/article/01782f13c138428bbb6e70260370c042","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"SoftwareX, Vol 30, Iss , Pp 102118- (2025)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1016/j.softx.2025.102118","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.softx.2025.102118","pdf_url":null,"source":{"id":"https://openalex.org/S2506067282","display_name":"SoftwareX","issn_l":"2352-7110","issn":["2352-7110"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"SoftwareX","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5173265043","display_name":null,"funder_award_id":"894489","funder_id":"https://openalex.org/F4320338337","funder_display_name":"H2020 Marie Sk\u0142odowska-Curie Actions"}],"funders":[{"id":"https://openalex.org/F4320332999","display_name":"Horizon 2020 Framework Programme","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320335254","display_name":"Horizon 2020","ror":null},{"id":"https://openalex.org/F4320338337","display_name":"H2020 Marie Sk\u0142odowska-Curie Actions","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W1031578623","https://openalex.org/W1970109618","https://openalex.org/W1984481443","https://openalex.org/W1988127920","https://openalex.org/W2021820673","https://openalex.org/W2029667189","https://openalex.org/W2103325328","https://openalex.org/W2111917512","https://openalex.org/W2132262459","https://openalex.org/W2139447954","https://openalex.org/W2397547384","https://openalex.org/W2540491215","https://openalex.org/W2564298127","https://openalex.org/W2788196490","https://openalex.org/W2949223833","https://openalex.org/W2972751083","https://openalex.org/W3035691127","https://openalex.org/W3046751266","https://openalex.org/W3197647196","https://openalex.org/W3201073812","https://openalex.org/W3208444451","https://openalex.org/W4391290994","https://openalex.org/W4396721167","https://openalex.org/W4403764140","https://openalex.org/W4404574243","https://openalex.org/W6675444167","https://openalex.org/W6874097891"],"related_works":["https://openalex.org/W2418291489","https://openalex.org/W3096519538","https://openalex.org/W2744747300","https://openalex.org/W4241166160","https://openalex.org/W2068121105","https://openalex.org/W2384826897","https://openalex.org/W1973516247","https://openalex.org/W1997466117","https://openalex.org/W2795695574","https://openalex.org/W2300282708"],"abstract_inverted_index":{"Despite":[0],"the":[1,7,15,45],"increasing":[2],"automation":[3],"of":[4,9,18,51,63,94],"workflows":[5],"for":[6,11,30,90],"preparation":[8],"systems":[10],"molecular":[12,19],"dynamics":[13],"simulations,":[14],"custom":[16],"editing":[17],"topologies":[20],"to":[21,72,78,80],"accommodate":[22],"non-standard":[23],"modifications":[24],"remains":[25],"a":[26,40,49,91],"daunting":[27],"task":[28],"even":[29],"experienced":[31],"users.":[32],"To":[33],"alleviate":[34],"this":[35],"issue,":[36],"we":[37],"created":[38],"Gromologist,":[39],"utility":[41],"library":[42,66],"that":[43],"provides":[44],"simulation":[46],"community":[47],"with":[48],"toolbox":[50],"primitive":[52],"operations,":[53],"as":[54,56],"well":[55],"useful":[57],"repetitive":[58],"procedures":[59],"identified":[60],"during":[61],"years":[62],"research.":[64],"The":[65,97],"has":[67],"been":[68],"developed":[69],"in":[70],"response":[71],"users\u2019":[73],"feedback,":[74],"and":[75,88,103],"will":[76],"continue":[77],"grow":[79],"include":[81],"more":[82],"use":[83],"cases,":[84],"thorough":[85],"automatic":[86],"testing":[87],"support":[89],"broader":[92],"spectrum":[93],"rare":[95],"features.":[96],"program":[98],"is":[99],"available":[100],"at":[101],"gitlab.com/KomBioMol/gromologist":[102],"via":[104],"Python\u2019s":[105],"pip.":[106]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":4}],"updated_date":"2026-05-24T08:33:08.758527","created_date":"2025-10-10T00:00:00"}
