{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,29]],"date-time":"2026-04-29T05:19:07Z","timestamp":1777439947687,"version":"3.51.4"},"reference-count":24,"publisher":"American Chemical Society (ACS)","issue":"18","license":[{"start":{"date-parts":[[2022,9,14]],"date-time":"2022-09-14T00:00:00Z","timestamp":1663113600000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001871","name":"Funda??o para a Ci?ncia e a Tecnologia","doi-asserted-by":"publisher","award":["LA\/P\/0087\/2020"],"award-info":[{"award-number":["LA\/P\/0087\/2020"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda??o para a Ci?ncia e a Tecnologia","doi-asserted-by":"publisher","award":["PTDC\/QUI-OUT\/29441\/2017"],"award-info":[{"award-number":["PTDC\/QUI-OUT\/29441\/2017"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda??o para a Ci?ncia e a Tecnologia","doi-asserted-by":"publisher","award":["SFRH\/BD\/144370\/2019"],"award-info":[{"award-number":["SFRH\/BD\/144370\/2019"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda??o para a Ci?ncia e a Tecnologia","doi-asserted-by":"publisher","award":["UIDB\/04612\/2020"],"award-info":[{"award-number":["UIDB\/04612\/2020"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda??o para a Ci?ncia e a Tecnologia","doi-asserted-by":"publisher","award":["UIDP\/04612\/2020"],"award-info":[{"award-number":["UIDP\/04612\/2020"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Chem. Inf. Model."],"published-print":{"date-parts":[[2022,9,26]]},"DOI":"10.1021\/acs.jcim.2c00823","type":"journal-article","created":{"date-parts":[[2022,9,14]],"date-time":"2022-09-14T20:08:46Z","timestamp":1663186126000},"page":"4435-4447","source":"Crossref","is-referenced-by-count":6,"title":["FixBox: A General Algorithm to Fix Molecular Systems in Periodic Boxes"],"prefix":"10.1021","volume":"62","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7044-1210","authenticated-orcid":true,"given":"Ant\u00f3nio M.","family":"Baptista","sequence":"first","affiliation":[{"name":"Instituto de Tecnologia Qu\u00edmica e Biol\u00f3gica Ant\u00f3nio Xavier, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6163-3184","authenticated-orcid":true,"given":"Lucie","family":"da Rocha","sequence":"additional","affiliation":[{"name":"Instituto de Tecnologia Qu\u00edmica e Biol\u00f3gica Ant\u00f3nio Xavier, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1020-6830","authenticated-orcid":true,"given":"Sara R. R.","family":"Campos","sequence":"additional","affiliation":[{"name":"Instituto de Tecnologia Qu\u00edmica e Biol\u00f3gica Ant\u00f3nio Xavier, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal"}]}],"member":"316","published-online":{"date-parts":[[2022,9,14]]},"reference":[{"key":"ref1\/cit1","volume-title":"Computer Simulation of Liquids","author":"Allen M. P.","year":"1987"},{"key":"ref2\/cit2","volume-title":"Molecular Modelling: Principles and Applications","author":"Leach A. R.","year":"2001","edition":"2"},{"key":"ref3\/cit3","doi-asserted-by":"publisher","DOI":"10.1063\/1.1497164"},{"key":"ref4\/cit4","doi-asserted-by":"publisher","DOI":"10.1021\/jp056456q"},{"key":"ref5\/cit5","unstructured":"GROMACS Development\nTeam.  GROMACS Documentation (Release\n2021.6). https:\/\/manual.gromacs.org\/documentation\/2021-current\/manual-2021.6.pdf, 2021."},{"key":"ref6\/cit6","unstructured":"Case, D.; Aktulga, H.; Belfon, K.; Ben-Shalom, I.; Brozell, S.; Cerutti, D.; Cheatham, T., III; Cisneros, G.; Cruzeiro, V.; Darden, T.; Duke, R.; Giambasu, G.; Gilson, M.; Gohlke, H.; Goetz, A.; Harris, R.; Izadi, S.; Izmailov, S.; Jin, C.; Kasavajhala, K.; Kaymak, M.; King, E.; Kovalenko, A.; Kurtzman, T.; Lee, T.; LeGrand, S.; Li, P.; Lin, C.; Liu, J.; Luchko, T.; Luo, R.; Machado, M.; Man, V.; Manathunga, M.; Merz, K.; Miao, Y.; Mikhailovskii, O.; Monard, G.; Nguyen, H.; O\u2019Hearn, K.; Onufriev, A.; Pan, F.; Pantano, S.; Qi, R.; Rahnamoun, A.; Roe, D.; Roitberg, A.; Sagui, C.; Schott-Verdugo, S.; Shen, J.; Simmerling, C.; Skrynnikov, N.; Smith, J.; Swails, J.; Walker, R.; Wang, J.; Wei, H.; Wolf, R.; Wu, X.; Xue, Y.; York, D.; Zhao, S.; Kollman, P. Amber 2021 Reference Manual. https:\/\/ambermd.org\/Manuals.php, 2021."},{"key":"ref7\/cit7","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw563"},{"key":"ref8\/cit8","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.1c00446"},{"key":"ref9\/cit9","volume-title":"Regular Figures","author":"T\u00f3th L. F.","year":"1964"},{"key":"ref10\/cit10","unstructured":"Adams, D. J. Alternatives to the periodic cube in computer simulation.  CCP5 Quarterly, 1983; Vol. 10, pp 30\u201336."},{"key":"ref11\/cit11","doi-asserted-by":"publisher","DOI":"10.1002\/(sici)1096-987x(19971130)18:15<1930::aid-jcc8>3.0.co;2-p"},{"key":"ref12\/cit12","volume-title":"Solid State Physics","author":"Ashcroft N. W.","year":"1976"},{"key":"ref13\/cit13","volume-title":"Statistical Mechanics: Theory and Molecular Simulation","author":"Tuckerman M. E.","year":"2010"},{"key":"ref14\/cit14","doi-asserted-by":"crossref","unstructured":"Gruber, P. M. Handbook of Convex Geometry; Gruber, P. M., Wills, J. M., Eds. North-Holland: Amsterdam, 1993; Chapter 3.1, pp 739\u2013763.","DOI":"10.1016\/B978-0-444-89597-4.50005-6"},{"key":"ref15\/cit15","volume-title":"Concrete Mathematics: A Foundation for Computer Science","author":"Graham R. L.","year":"1994","edition":"2"},{"key":"ref16\/cit16","unstructured":"Wassenaar, T. A. Molecular Dynamics of Sense and Sensibility in Processing and Analysis of Data. Ph.D. thesis; University of Groningen: Groningen, 2006."},{"key":"ref17\/cit17","volume-title":"Geometric Transformations","volume":"1","author":"Modenov P. S.","year":"1965"},{"key":"ref18\/cit18","volume-title":"Principles of Topology","author":"Croom F. H.","year":"1989"},{"key":"ref19\/cit19","volume-title":"A First Course in Graph Theory","author":"Chartrand G.","year":"2012"},{"key":"ref20\/cit20","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.1c01187"},{"key":"ref21\/cit21","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-020-77040-y"},{"key":"ref22\/cit22","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-06488-4"},{"key":"ref23\/cit23","doi-asserted-by":"publisher","DOI":"10.4208\/cicp.300611.201011s"},{"key":"ref24\/cit24","doi-asserted-by":"publisher","DOI":"10.1002\/pro.3280"}],"container-title":["Journal of Chemical Information and Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.2c00823","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.2c00823","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,4,27]],"date-time":"2023-04-27T05:03:51Z","timestamp":1682571831000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.jcim.2c00823"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,9,14]]},"references-count":24,"journal-issue":{"issue":"18","published-print":{"date-parts":[[2022,9,26]]}},"alternative-id":["10.1021\/acs.jcim.2c00823"],"URL":"https:\/\/doi.org\/10.1021\/acs.jcim.2c00823","relation":{},"ISSN":["1549-9596","1549-960X"],"issn-type":[{"value":"1549-9596","type":"print"},{"value":"1549-960X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,9,14]]}}}