{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T18:34:51Z","timestamp":1790274891019,"version":"4.1.0"},"reference-count":62,"publisher":"American Chemical Society (ACS)","issue":"3","license":[{"start":{"date-parts":[[2024,1,12]],"date-time":"2024-01-12T00:00:00Z","timestamp":1705017600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004359","name":"Vetenskapsr?det","doi-asserted-by":"publisher","award":["2019-04477"],"award-info":[{"award-number":["2019-04477"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002341","name":"Academy of Finland","doi-asserted-by":"publisher","award":["332743"],"award-info":[{"award-number":["332743"]}],"id":[{"id":"10.13039\/501100002341","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002341","name":"Academy of Finland","doi-asserted-by":"publisher","award":["342908"],"award-info":[{"award-number":["342908"]}],"id":[{"id":"10.13039\/501100002341","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002341","name":"Academy of Finland","doi-asserted-by":"publisher","award":["311031"],"award-info":[{"award-number":["311031"]}],"id":[{"id":"10.13039\/501100002341","id-type":"DOI","asserted-by":"publisher"}]},{"name":"BioExcel","award":["H2020-INFRAEDI-02-2018-823830"],"award-info":[{"award-number":["H2020-INFRAEDI-02-2018-823830"]}]},{"name":"BioExcel","award":["101093290"],"award-info":[{"award-number":["101093290"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Chem. Inf. Model."],"published-print":{"date-parts":[[2024,2,12]]},"DOI":"10.1021\/acs.jcim.3c01313","type":"journal-article","created":{"date-parts":[[2024,1,12]],"date-time":"2024-01-12T15:03:51Z","timestamp":1705071831000},"page":"567-574","source":"Crossref","is-referenced-by-count":61,"title":["phbuilder: A Tool for Efficiently Setting up Constant pH Molecular Dynamics Simulations in GROMACS"],"prefix":"10.1021","volume":"64","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2835-7987","authenticated-orcid":true,"given":"Anton","family":"Jansen","sequence":"first","affiliation":[{"name":"Department of Applied Physics and Swedish e-Science Research Center, Science for Life Laboratory, KTH Royal Institute of Technology, 100 44 Stockholm, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-1243-0215","authenticated-orcid":true,"given":"Noora","family":"Aho","sequence":"additional","affiliation":[{"name":"Nanoscience Center and Department of Chemistry, University of Jyv\u00e4skyl\u00e4, 40014 Jyv\u00e4skyl\u00e4, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8148-5334","authenticated-orcid":true,"given":"Gerrit","family":"Groenhof","sequence":"additional","affiliation":[{"name":"Nanoscience Center and Department of Chemistry, University of Jyv\u00e4skyl\u00e4, 40014 Jyv\u00e4skyl\u00e4, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2031-4691","authenticated-orcid":true,"given":"Pavel","family":"Buslaev","sequence":"additional","affiliation":[{"name":"Nanoscience Center and Department of Chemistry, University of Jyv\u00e4skyl\u00e4, 40014 Jyv\u00e4skyl\u00e4, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Berk","family":"Hess","sequence":"additional","affiliation":[{"name":"Department of Applied Physics and Swedish e-Science Research Center, Science for Life Laboratory, KTH Royal Institute of Technology, 100 44 Stockholm, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2024,1,12]]},"reference":[{"key":"ref1\/cit1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1208351"},{"key":"ref2\/cit2","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.7b00564"},{"key":"ref3\/cit3","doi-asserted-by":"publisher","DOI":"10.1007\/s12551-017-0311-5"},{"key":"ref4\/cit4","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1097-0134(199704)27:4<523::AID-PROT6>3.0.CO;2-B"},{"key":"ref5\/cit5","doi-asserted-by":"publisher","DOI":"10.1063\/1.1497164"},{"key":"ref6\/cit6","doi-asserted-by":"publisher","DOI":"10.1002\/prot.10046"},{"key":"ref7\/cit7","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.20139"},{"key":"ref8\/cit8","doi-asserted-by":"publisher","DOI":"10.1021\/ct900676b"},{"key":"ref9\/cit9","doi-asserted-by":"publisher","DOI":"10.1002\/prot.23176"},{"key":"ref10\/cit10","doi-asserted-by":"publisher","DOI":"10.1021\/ct401042b"},{"key":"ref11\/cit11","doi-asserted-by":"publisher","DOI":"10.1021\/ct300512h"},{"key":"ref12\/cit12","doi-asserted-by":"publisher","DOI":"10.1063\/1.1370959"},{"key":"ref13\/cit13","doi-asserted-by":"publisher","DOI":"10.1002\/prot.20128"},{"key":"ref14\/cit14","doi-asserted-by":"publisher","DOI":"10.1529\/biophysj.105.061341"},{"key":"ref15\/cit15","doi-asserted-by":"publisher","DOI":"10.1021\/ct200061r"},{"key":"ref16\/cit16","doi-asserted-by":"publisher","DOI":"10.1021\/ct200146j"},{"key":"ref17\/cit17","doi-asserted-by":"publisher","DOI":"10.1063\/1.4766352"},{"key":"ref18\/cit18","doi-asserted-by":"publisher","DOI":"10.1021\/ct2006314"},{"key":"ref19\/cit19","doi-asserted-by":"publisher","DOI":"10.1016\/j.bpj.2013.06.036"},{"key":"ref20\/cit20","doi-asserted-by":"publisher","DOI":"10.1021\/ct500175m"},{"key":"ref21\/cit21","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.6b00807"},{"key":"ref22\/cit22","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.6b00552"},{"key":"ref23\/cit23","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.8b00227"},{"key":"ref24\/cit24","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.9b00754"},{"key":"ref25\/cit25","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.0c00258"},{"key":"ref26\/cit26","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.2c00586"},{"key":"ref27\/cit27","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.2c00516"},{"key":"ref28\/cit28","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.2c00517"},{"key":"ref29\/cit29","doi-asserted-by":"publisher","DOI":"10.1016\/j.softx.2015.06.001"},{"key":"ref30\/cit30","doi-asserted-by":"publisher","DOI":"10.1063\/1.472109"},{"key":"ref31\/cit31","doi-asserted-by":"publisher","DOI":"10.33011\/livecoms.4.1.1563"},{"key":"ref32\/cit32","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.20945"},{"key":"ref33\/cit33","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.21224"},{"key":"ref34\/cit34","doi-asserted-by":"publisher","DOI":"10.21105\/joss.01831"},{"key":"ref35\/cit35","doi-asserted-by":"publisher","DOI":"10.1186\/s13321-019-0348-5"},{"key":"ref36\/cit36","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.23218"},{"key":"ref37\/cit37","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.9b01158"},{"key":"ref38\/cit38","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.1c00194"},{"key":"ref39\/cit39","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.5b00368"},{"key":"ref40\/cit40","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.0c00884"},{"key":"ref41\/cit41","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.23354"},{"key":"ref42\/cit42","doi-asserted-by":"publisher","DOI":"10.1021\/ct400626b"},{"key":"ref43\/cit43","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.5b01160"},{"key":"ref44\/cit44","volume-title":"GROMACS constant pH manual","author":"Buslaev P."},{"key":"ref45\/cit45","doi-asserted-by":"publisher","DOI":"10.1063\/1.1749657"},{"key":"ref46\/cit46","doi-asserted-by":"publisher","DOI":"10.1063\/1.1873592"},{"key":"ref47\/cit47","doi-asserted-by":"publisher","DOI":"10.1021\/ct2003995"},{"key":"ref48\/cit48","doi-asserted-by":"publisher","DOI":"10.1021\/bi00082a026"},{"key":"ref49\/cit49","doi-asserted-by":"publisher","DOI":"10.1021\/bi00196a004"},{"key":"ref50\/cit50","doi-asserted-by":"publisher","DOI":"10.26508\/lsa.202101011"},{"key":"ref51\/cit51","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/28.1.235"},{"key":"ref52\/cit52","doi-asserted-by":"publisher","DOI":"10.1021\/ct049849m"},{"key":"ref53\/cit53","doi-asserted-by":"publisher","DOI":"10.1021\/j100059a038"},{"key":"ref54\/cit54","doi-asserted-by":"publisher","DOI":"10.1063\/1.472061"},{"key":"ref55\/cit55","doi-asserted-by":"publisher","DOI":"10.1063\/1.464397"},{"key":"ref56\/cit56","doi-asserted-by":"publisher","DOI":"10.1063\/1.470117"},{"key":"ref57\/cit57","doi-asserted-by":"publisher","DOI":"10.1063\/1.2408420"},{"key":"ref58\/cit58","doi-asserted-by":"publisher","DOI":"10.1063\/5.0020514"},{"key":"ref59\/cit59","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H"},{"key":"ref60\/cit60","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540130805"},{"key":"ref61\/cit61","doi-asserted-by":"publisher","DOI":"10.1021\/ci3000453"},{"key":"ref62\/cit62","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.21507"}],"container-title":["Journal of Chemical Information and Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.3c01313","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.3c01313","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,12]],"date-time":"2024-02-12T04:12:34Z","timestamp":1707711154000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.jcim.3c01313"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,1,12]]},"references-count":62,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2024,2,12]]}},"alternative-id":["10.1021\/acs.jcim.3c01313"],"URL":"https:\/\/doi.org\/10.1021\/acs.jcim.3c01313","relation":{"has-preprint":[{"id-type":"doi","id":"10.26434\/chemrxiv-2023-rdhjn","asserted-by":"object"}]},"ISSN":["1549-9596","1549-960X"],"issn-type":[{"value":"1549-9596","type":"print"},{"value":"1549-960X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,1,12]]}}}