{"id":"https://openalex.org/W3080868448","doi":"https://doi.org/10.1021/acs.jcim.0c00648","title":"grand: A Python Module for Grand Canonical Water Sampling in OpenMM","display_name":"grand: A Python Module for Grand Canonical Water Sampling in OpenMM","publication_year":2020,"publication_date":"2020-08-24","ids":{"openalex":"https://openalex.org/W3080868448","doi":"https://doi.org/10.1021/acs.jcim.0c00648","mag":"3080868448","pmid":"https://pubmed.ncbi.nlm.nih.gov/32835483"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.0c00648","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.0c00648","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://eprints.soton.ac.uk/444466/1/manuscript.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5004538694","display_name":"Marley L. Samways","orcid":"https://orcid.org/0000-0001-9431-8789"},"institutions":[{"id":"https://openalex.org/I43439940","display_name":"University of Southampton","ror":"https://ror.org/01ryk1543","country_code":"GB","type":"education","lineage":["https://openalex.org/I43439940"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Marley L. Samways","raw_affiliation_strings":["School of Chemistry, University of Southampton, Southampton, SO17 1BJ, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0001-9431-8789","affiliations":[{"raw_affiliation_string":"School of Chemistry, University of Southampton, Southampton, SO17 1BJ, United Kingdom","institution_ids":["https://openalex.org/I43439940"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040045526","display_name":"Hannah E. Bruce Macdonald","orcid":"https://orcid.org/0000-0002-5562-6866"},"institutions":[{"id":"https://openalex.org/I1334819555","display_name":"Memorial Sloan Kettering Cancer Center","ror":"https://ror.org/02yrq0923","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1334819555"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hannah E. Bruce Macdonald","raw_affiliation_strings":["Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States"],"raw_orcid":"https://orcid.org/0000-0002-5562-6866","affiliations":[{"raw_affiliation_string":"Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States","institution_ids":["https://openalex.org/I1334819555"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5067820273","display_name":"Jonathan W. Essex","orcid":"https://orcid.org/0000-0003-2639-2746"},"institutions":[{"id":"https://openalex.org/I43439940","display_name":"University of Southampton","ror":"https://ror.org/01ryk1543","country_code":"GB","type":"education","lineage":["https://openalex.org/I43439940"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Jonathan W. Essex","raw_affiliation_strings":["School of Chemistry, University of Southampton, Southampton, SO17 1BJ, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0003-2639-2746","affiliations":[{"raw_affiliation_string":"School of Chemistry, University of Southampton, Southampton, SO17 1BJ, United Kingdom","institution_ids":["https://openalex.org/I43439940"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5067820273"],"corresponding_institution_ids":["https://openalex.org/I43439940"],"apc_list":null,"apc_paid":null,"fwci":2.3848,"has_fulltext":true,"cited_by_count":46,"citation_normalized_percentile":{"value":0.89926691,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"60","issue":"10","first_page":"4436","last_page":"4441"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9994999766349792,"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":0.9994999766349792,"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/T10411","display_name":"Proteins in Food Systems","score":0.9678000211715698,"subfield":{"id":"https://openalex.org/subfields/1106","display_name":"Food Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10407","display_name":"Lipid Membrane Structure and Behavior","score":0.964900016784668,"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/python","display_name":"Python (programming language)","score":0.8740349411964417},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.7303933501243591},{"id":"https://openalex.org/keywords/grand-canonical-ensemble","display_name":"Grand canonical ensemble","score":0.681813657283783},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5671697854995728},{"id":"https://openalex.org/keywords/grand-challenges","display_name":"Grand Challenges","score":0.5670527219772339},{"id":"https://openalex.org/keywords/monte-carlo-method","display_name":"Monte Carlo method","score":0.5474267601966858},{"id":"https://openalex.org/keywords/sampling","display_name":"Sampling (signal processing)","score":0.432037889957428},{"id":"https://openalex.org/keywords/canonical-ensemble","display_name":"Canonical ensemble","score":0.4128260314464569},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.3949279487133026},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.32339391112327576},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.3210216760635376},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.2519516944885254},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.202825665473938},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.1736297607421875},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.10361048579216003}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8740349411964417},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.7303933501243591},{"id":"https://openalex.org/C29235156","wikidata":"https://www.wikidata.org/wiki/Q1153553","display_name":"Grand canonical ensemble","level":3,"score":0.681813657283783},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5671697854995728},{"id":"https://openalex.org/C2777362162","wikidata":"https://www.wikidata.org/wiki/Q5594431","display_name":"Grand Challenges","level":2,"score":0.5670527219772339},{"id":"https://openalex.org/C19499675","wikidata":"https://www.wikidata.org/wiki/Q232207","display_name":"Monte Carlo method","level":2,"score":0.5474267601966858},{"id":"https://openalex.org/C140779682","wikidata":"https://www.wikidata.org/wiki/Q210868","display_name":"Sampling (signal processing)","level":3,"score":0.432037889957428},{"id":"https://openalex.org/C28556851","wikidata":"https://www.wikidata.org/wiki/Q1077753","display_name":"Canonical ensemble","level":3,"score":0.4128260314464569},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.3949279487133026},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.32339391112327576},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.3210216760635376},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.2519516944885254},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.202825665473938},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.1736297607421875},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.10361048579216003},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"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/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002417","descriptor_name":"Cattle","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002417","descriptor_name":"Cattle","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002417","descriptor_name":"Cattle","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","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":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014867","descriptor_name":"Water","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.0c00648","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.0c00648","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:32835483","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32835483","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:eprints.soton.ac.uk:444466","is_oa":true,"landing_page_url":"https://eprints.soton.ac.uk/444466/1/manuscript.pdf","pdf_url":"https://eprints.soton.ac.uk/444466/1/manuscript.pdf","source":{"id":"https://openalex.org/S4306401019","display_name":"ePrints Soton (University of Southampton)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I43439940","host_organization_name":"University of Southampton","host_organization_lineage":["https://openalex.org/I43439940"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"}],"best_oa_location":{"id":"pmh:oai:eprints.soton.ac.uk:444466","is_oa":true,"landing_page_url":"https://eprints.soton.ac.uk/444466/1/manuscript.pdf","pdf_url":"https://eprints.soton.ac.uk/444466/1/manuscript.pdf","source":{"id":"https://openalex.org/S4306401019","display_name":"ePrints Soton (University of Southampton)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I43439940","host_organization_name":"University of Southampton","host_organization_lineage":["https://openalex.org/I43439940"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"},"sustainable_development_goals":[{"score":0.8399999737739563,"id":"https://metadata.un.org/sdg/6","display_name":"Clean water and sanitation"}],"awards":[{"id":"https://openalex.org/G105296940","display_name":"CCP-BioSim: Biomolecular simulation at the life sciences interface","funder_award_id":"EP/J010189/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G2143813100","display_name":"EPSRC Centre for Doctoral Training in Next Generation Computational Modelling","funder_award_id":"EP/L015382/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G4078605609","display_name":null,"funder_award_id":"EP/L015382/1","funder_id":"https://openalex.org/F4320320277","funder_display_name":"University of Southampton"},{"id":"https://openalex.org/G4706702539","display_name":"CCP-BioSim: Biomolecular Simulation at the Life Sciences Interface","funder_award_id":"EP/M022609/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G5758995618","display_name":null,"funder_award_id":"EP/M022609/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G6610335126","display_name":null,"funder_award_id":"EP/L015382/","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G8008707186","display_name":null,"funder_award_id":"EP/J010189/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320320277","display_name":"University of Southampton","ror":"https://ror.org/01ryk1543"},{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3080868448.pdf","grobid_xml":"https://content.openalex.org/works/W3080868448.grobid-xml"},"referenced_works_count":44,"referenced_works":["https://openalex.org/W1966495701","https://openalex.org/W1971556338","https://openalex.org/W1976499671","https://openalex.org/W1981225934","https://openalex.org/W1983066351","https://openalex.org/W1996541029","https://openalex.org/W1998591815","https://openalex.org/W2007143784","https://openalex.org/W2014433873","https://openalex.org/W2021929941","https://openalex.org/W2031990249","https://openalex.org/W2032456809","https://openalex.org/W2032598923","https://openalex.org/W2035374663","https://openalex.org/W2039127550","https://openalex.org/W2056211855","https://openalex.org/W2058834481","https://openalex.org/W2063115321","https://openalex.org/W2067174909","https://openalex.org/W2078469621","https://openalex.org/W2090338420","https://openalex.org/W2103945336","https://openalex.org/W2106140689","https://openalex.org/W2122425162","https://openalex.org/W2146650190","https://openalex.org/W2156283242","https://openalex.org/W2157135163","https://openalex.org/W2158272796","https://openalex.org/W2228949267","https://openalex.org/W2335901641","https://openalex.org/W2404280981","https://openalex.org/W2566501678","https://openalex.org/W2594816406","https://openalex.org/W2765296481","https://openalex.org/W2808209498","https://openalex.org/W2895846624","https://openalex.org/W2900735593","https://openalex.org/W2908766165","https://openalex.org/W2921674955","https://openalex.org/W2949223833","https://openalex.org/W2950438613","https://openalex.org/W2973013892","https://openalex.org/W2996021258","https://openalex.org/W3101060993"],"related_works":["https://openalex.org/W2093935103","https://openalex.org/W2065334534","https://openalex.org/W2360340668","https://openalex.org/W2786740239","https://openalex.org/W2035965523","https://openalex.org/W2564354043","https://openalex.org/W3102493577","https://openalex.org/W2271549193","https://openalex.org/W2022890967","https://openalex.org/W2081516048"],"abstract_inverted_index":{"Networks":[0],"of":[1,26,92,99,108],"water":[2,28,101,122],"molecules":[3],"can":[4,14],"play":[5],"a":[6],"critical":[7],"role":[8],"at":[9],"the":[10,24,48,52,84,90,97,112],"protein\u2013ligand":[11],"interface":[12],"and":[13,45],"directly":[15],"influence":[16],"drug\u2013target":[17],"interactions.":[18],"Grand":[19],"canonical":[20,79],"methods":[21],"aid":[22],"in":[23,75],"sampling":[25],"these":[27],"molecules,":[29],"where":[30],"conventional":[31,129],"molecular":[32,69,130],"dynamics":[33,70],"equilibration":[34],"times":[35],"are":[36,125],"often":[37],"long,":[38],"by":[39,95],"allowing":[40],"waters":[41],"to":[42,51,72,111],"be":[43,73],"inserted":[44],"deleted":[46],"from":[47,103],"system,":[49],"according":[50],"chemical":[53],"potential.":[54],"Here,":[55],"we":[56],"present":[57],"our":[58],"open":[59],"source":[60],"Python":[61],"module,":[62],"grand":[63,78],"(":[64],"https://github.com/essex-lab/grand":[65],"),":[66],"which":[67],"allows":[68],"simulations":[71],"performed":[74],"conjunction":[76],"with":[77],"Monte":[80],"Carlo":[81],"sampling,":[82],"using":[83,128],"OpenMM":[85],"simulation":[86],"engine.":[87],"We":[88],"demonstrate":[89],"accuracy":[91],"this":[93,109],"module":[94],"reproducing":[96],"density":[98],"bulk":[100],"observed":[102],"constant":[104],"pressure":[105],"simulations.":[106],"Application":[107],"code":[110],"bovine":[113],"pancreatic":[114],"trypsin":[115],"inhibitor":[116],"protein":[117],"reproduces":[118],"three":[119],"buried":[120],"crystallographic":[121],"sites":[123],"that":[124],"poorly":[126],"sampled":[127],"dynamics.":[131]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":12},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":2}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}
