{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T06:06:02Z","timestamp":1783490762052,"version":"3.55.0"},"reference-count":294,"publisher":"AIP Publishing","issue":"3","funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["2237792"],"award-info":[{"award-number":["2237792"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000181","name":"Air Force Office of Scientific Research","doi-asserted-by":"publisher","award":["FA9550-22-1-0025"],"award-info":[{"award-number":["FA9550-22-1-0025"]}],"id":[{"id":"10.13039\/100000181","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["pubs.aip.org"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2024,7,21]]},"abstract":"<jats:p>PyDFT-QMMM is a Python-based package for performing hybrid quantum mechanics\/molecular mechanics (QM\/MM) simulations at the density functional level of theory. The program is designed to treat short-range and long-range interactions through user-specified combinations of electrostatic and mechanical embedding procedures within periodic simulation domains, providing necessary interfaces to external quantum chemistry and molecular dynamics software. To enable direct embedding of long-range electrostatics in periodic systems, we have derived and implemented force terms for our previously described QM\/MM\/PME approach [Pederson and McDaniel, J. Chem. Phys. 156, 174105 (2022)]. Communication with external software packages Psi4 and OpenMM is facilitated through Python application programming interfaces (APIs). The core library contains basic utilities for running QM\/MM molecular dynamics simulations, and plug-in entry-points are provided for users to implement custom energy\/force calculation and integration routines, within an extensible architecture. The user interacts with PyDFT-QMMM primarily through its Python API, allowing for complex workflow development with Python scripting, for example, interfacing with PLUMED for free energy simulations. We provide benchmarks of forces and energy conservation for the QM\/MM\/PME and alternative QM\/MM electrostatic embedding approaches. We further demonstrate a simple example use case for water solute in a water solvent system, for which radial distribution functions are computed from 100\u00a0ps QM\/MM simulations; in this example, we highlight how the solvation structure is sensitive to different basis-set choices due to under- or over-polarization of the QM water molecule\u2019s electron density.<\/jats:p>","DOI":"10.1063\/5.0219851","type":"journal-article","created":{"date-parts":[[2024,7,15]],"date-time":"2024-07-15T10:22:44Z","timestamp":1721038964000},"update-policy":"https:\/\/doi.org\/10.1063\/aip-crossmark-policy-page","source":"Crossref","is-referenced-by-count":13,"title":["PyDFT-QMMM: A modular, extensible software framework for DFT-based QM\/MM molecular dynamics"],"prefix":"10.1063","volume":"161","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6718-3823","authenticated-orcid":false,"given":"John P.","family":"Pederson","sequence":"first","affiliation":[{"name":"School of Chemistry and Biochemistry, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9211-1108","authenticated-orcid":false,"given":"Jesse G.","family":"McDaniel","sequence":"additional","affiliation":[{"name":"School of Chemistry and Biochemistry, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"317","published-online":{"date-parts":[[2024,7,15]]},"reference":[{"key":"2024071510214127200_c1","doi-asserted-by":"publisher","first-page":"298","DOI":"10.1021\/ar950140r","volume":"29","year":"1996","journal-title":"Acc. Chem. Res."},{"key":"2024071510214127200_c2","doi-asserted-by":"publisher","first-page":"118","DOI":"10.1007\/s11244-021-01520-2","volume":"65","year":"2022","journal-title":"Top. Catal."},{"key":"2024071510214127200_c3","first-page":"59","volume-title":"Advances in Quantum Chemistry","year":"2010"},{"key":"2024071510214127200_c4","doi-asserted-by":"publisher","first-page":"1599","DOI":"10.1021\/acs.joc.1c03148","volume":"87","year":"2022","journal-title":"J.\u00a0Org. Chem."},{"key":"2024071510214127200_c5","doi-asserted-by":"publisher","first-page":"e4202","DOI":"10.1002\/poc.4202","volume":"34","year":"2021","journal-title":"J.\u00a0Phys. Org. Chem."},{"key":"2024071510214127200_c6","doi-asserted-by":"publisher","first-page":"1841","DOI":"10.1021\/acs.jctc.7b01206","volume":"14","year":"2018","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c7","doi-asserted-by":"publisher","first-page":"041303","DOI":"10.1063\/5.0064075","volume":"2","year":"2021","journal-title":"Chem. Phys. Rev."},{"key":"2024071510214127200_c8","doi-asserted-by":"publisher","first-page":"e25558","DOI":"10.1002\/qua.25558","volume":"118","year":"2018","journal-title":"Int. J. Quantum Chem."},{"key":"2024071510214127200_c9","doi-asserted-by":"publisher","first-page":"e1656","DOI":"10.1002\/wcms.1656","volume":"13","year":"2023","journal-title":"WIREs Comput. Mol. Sci."},{"key":"2024071510214127200_c10","doi-asserted-by":"publisher","first-page":"2660","DOI":"10.3390\/molecules27092660","volume":"27","year":"2022","journal-title":"Molecules"},{"key":"2024071510214127200_c11","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1016\/j.sbi.2021.07.004","volume":"72","year":"2022","journal-title":"Curr. Opin. Struct. Biol."},{"key":"2024071510214127200_c12","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1002\/wcms.1519","volume":"11","year":"2021","journal-title":"WIREs Comput. Mol. Sci."},{"key":"2024071510214127200_c13","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1016\/0301-0104(81)85090-2","volume":"55","year":"1981","journal-title":"Chem. Phys."},{"key":"2024071510214127200_c14","doi-asserted-by":"publisher","first-page":"3032","DOI":"10.1063\/1.474659","volume":"107","year":"1997","journal-title":"J.\u00a0Chem. Phys."},{"key":"2024071510214127200_c15","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1063\/1.1376127","volume":"115","year":"2001","journal-title":"J.\u00a0Chem. Phys."},{"key":"2024071510214127200_c16","doi-asserted-by":"publisher","first-page":"1198","DOI":"10.1002\/anie.200802019","volume":"48","year":"2009","journal-title":"Angew. Chem., Int. Ed."},{"key":"2024071510214127200_c17","volume-title":"QM\/MM Methods","year":"2024"},{"key":"2024071510214127200_c18","doi-asserted-by":"publisher","first-page":"e1440","DOI":"10.1002\/wcms.1440","volume":"10","year":"2020","journal-title":"WIREs Comput. Mol. Sci."},{"key":"2024071510214127200_c19","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1002\/wcms.13","volume":"1","year":"2011","journal-title":"WIREs Comput. Mol. Sci."},{"key":"2024071510214127200_c20","doi-asserted-by":"publisher","first-page":"014905","DOI":"10.1063\/1.1940047","volume":"123","year":"2005","journal-title":"J.\u00a0Chem. Phys."},{"key":"2024071510214127200_c21","doi-asserted-by":"publisher","first-page":"3114","DOI":"10.1021\/ct900437b","volume":"5","year":"2009","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c22","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1021\/ct1005455","volume":"7","year":"2011","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c23","doi-asserted-by":"publisher","first-page":"e1515","DOI":"10.1002\/wcms.1515","volume":"11","year":"2021","journal-title":"WIREs Comput. Mol. Sci."},{"key":"2024071510214127200_c24","doi-asserted-by":"publisher","first-page":"12522","DOI":"10.1021\/jp308218m","volume":"116","year":"2012","journal-title":"J.\u00a0Phys. Chem. B"},{"key":"2024071510214127200_c25","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1002\/qua.1410","volume":"84","year":"2001","journal-title":"Int. J. Quantum Chem."},{"key":"2024071510214127200_c26","doi-asserted-by":"publisher","first-page":"1532","DOI":"10.1002\/qua.25199","volume":"116","year":"2016","journal-title":"Int. J. Quantum Chem."},{"key":"2024071510214127200_c27","doi-asserted-by":"publisher","first-page":"5580","DOI":"10.1021\/acs.jpca.9b03995","volume":"123","year":"2019","journal-title":"J.\u00a0Phys. Chem. A"},{"key":"2024071510214127200_c28","doi-asserted-by":"publisher","first-page":"15706","DOI":"10.1039\/c9nj04003j","volume":"43","year":"2019","journal-title":"New J. Chem."},{"key":"2024071510214127200_c29","doi-asserted-by":"publisher","first-page":"116","DOI":"10.3389\/fchem.2018.00116","volume":"6","year":"2018","journal-title":"Front. Chem."},{"key":"2024071510214127200_c30","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1021\/ar900171c","volume":"43","year":"2010","journal-title":"Acc. Chem. Res."},{"key":"2024071510214127200_c31","doi-asserted-by":"publisher","first-page":"5606","DOI":"10.1021\/acs.jctc.5b01029","volume":"11","year":"2015","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c32","doi-asserted-by":"publisher","first-page":"2087","DOI":"10.1021\/acs.jpcb.1c10200","volume":"126","year":"2022","journal-title":"J.\u00a0Phys. Chem. B"},{"key":"2024071510214127200_c33","doi-asserted-by":"publisher","first-page":"5067","DOI":"10.1039\/c7cp08696b","volume":"20","year":"2018","journal-title":"Phys. Chem. Chem. Phys."},{"key":"2024071510214127200_c34","doi-asserted-by":"publisher","first-page":"2644","DOI":"10.1021\/jp312229b","volume":"117","year":"2013","journal-title":"J.\u00a0Phys. Chem. A"},{"key":"2024071510214127200_c35","doi-asserted-by":"publisher","first-page":"525","DOI":"10.1146\/annurev-biophys-111622-091140","volume":"52","year":"2023","journal-title":"Annu. Rev. Biophys."},{"key":"2024071510214127200_c36","doi-asserted-by":"publisher","first-page":"e202200799","DOI":"10.1002\/cbic.202300300","volume":"24","year":"2023","journal-title":"ChemBioChem"},{"key":"2024071510214127200_c37","doi-asserted-by":"publisher","first-page":"6217","DOI":"10.1021\/cr500628b","volume":"115","year":"2015","journal-title":"Chem. Rev."},{"key":"2024071510214127200_c38","doi-asserted-by":"publisher","first-page":"2188","DOI":"10.1021\/acscatal.7b04367","volume":"8","year":"2018","journal-title":"ACS Catal."},{"key":"2024071510214127200_c39","doi-asserted-by":"publisher","first-page":"695","DOI":"10.1002\/qua.20032","volume":"99","year":"2004","journal-title":"Int. J. Quantum Chem."},{"key":"2024071510214127200_c40","doi-asserted-by":"publisher","first-page":"182","DOI":"10.3389\/fchem.2019.00182","volume":"7","year":"2019","journal-title":"Front. Chem."},{"key":"2024071510214127200_c41","doi-asserted-by":"publisher","first-page":"296","DOI":"10.1039\/b913356a","volume":"39","year":"2010","journal-title":"Dalton Trans."},{"key":"2024071510214127200_c42","doi-asserted-by":"publisher","first-page":"3c00080","DOI":"10.1021\/acsphyschemau.3c00080","volume":"4","year":"2024","journal-title":"ACS Phys. Chem. Au"},{"key":"2024071510214127200_c43","doi-asserted-by":"publisher","first-page":"20130377","DOI":"10.1098\/rsta.2013.0377","volume":"372","year":"2014","journal-title":"Philos. Trans. R. Soc., A"},{"key":"2024071510214127200_c44","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1007\/s00214-006-0143-z","volume":"117","year":"2007","journal-title":"Theor. Chem. Acc."},{"key":"2024071510214127200_c45","doi-asserted-by":"publisher","first-page":"414","DOI":"10.1021\/ct700296x","volume":"4","year":"2008","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c46","doi-asserted-by":"publisher","first-page":"168","DOI":"10.1080\/08927022.2014.911870","volume":"41","year":"2015","journal-title":"Mol. Simul."},{"key":"2024071510214127200_c47","doi-asserted-by":"publisher","first-page":"2609","DOI":"10.1021\/acs.jcim.2c01522","volume":"63","year":"2023","journal-title":"J.\u00a0Chem. Inf. Model."},{"key":"2024071510214127200_c48","doi-asserted-by":"publisher","first-page":"3647","DOI":"10.1021\/acs.jcim.3c00557","volume":"63","year":"2023","journal-title":"J.\u00a0Chem. Inf. Model."},{"key":"2024071510214127200_c49","doi-asserted-by":"publisher","first-page":"6562","DOI":"10.1039\/d2cp04537k","volume":"25","year":"2023","journal-title":"Phys. Chem. Chem. Phys."},{"key":"2024071510214127200_c50","doi-asserted-by":"publisher","first-page":"2530","DOI":"10.1021\/acs.jctc.1c00714","volume":"18","year":"2022","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c51","doi-asserted-by":"publisher","first-page":"9913","DOI":"10.1021\/acs.jpcb.6b07203","volume":"120","year":"2016","journal-title":"J.\u00a0Phys. Chem. B"},{"key":"2024071510214127200_c52","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1002\/wcms.1161","volume":"4","year":"2014","journal-title":"WIREs Comput. Mol. Sci."},{"key":"2024071510214127200_c53","doi-asserted-by":"publisher","first-page":"5609","DOI":"10.1021\/jp069056r","volume":"111","year":"2007","journal-title":"J.\u00a0Phys. Chem. A"},{"key":"2024071510214127200_c54","doi-asserted-by":"publisher","first-page":"1710252","DOI":"10.1080\/23746149.2019.1710252","volume":"5","year":"2020","journal-title":"Adv. Phys.: X"},{"key":"2024071510214127200_c55","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1002\/wcms.10","volume":"1","year":"2011","journal-title":"WIREs Comput. Mol. Sci."},{"key":"2024071510214127200_c56","doi-asserted-by":"publisher","first-page":"563","DOI":"10.1021\/acs.jctc.6b01049","volume":"13","year":"2017","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c57","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1021\/acs.jctc.1c00878","volume":"18","year":"2022","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c58","doi-asserted-by":"publisher","first-page":"3524","DOI":"10.1021\/acs.jctc.8b00348","volume":"14","year":"2018","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c59","doi-asserted-by":"publisher","first-page":"3531","DOI":"10.1063\/1.1383795","volume":"115","year":"2001","journal-title":"J.\u00a0Chem. Phys."},{"key":"2024071510214127200_c60","doi-asserted-by":"publisher","first-page":"335201","DOI":"10.1088\/0953-8984\/28\/33\/335201","volume":"28","year":"2016","journal-title":"J.\u00a0Phys.: Condens. Matter"},{"key":"2024071510214127200_c61","doi-asserted-by":"publisher","first-page":"10452","DOI":"10.1063\/1.479049","volume":"110","year":"1999","journal-title":"J.\u00a0Chem. Phys."},{"key":"2024071510214127200_c62","doi-asserted-by":"publisher","first-page":"6941","DOI":"10.1063\/1.1462041","volume":"116","year":"2002","journal-title":"J.\u00a0Chem. Phys."},{"key":"2024071510214127200_c63","doi-asserted-by":"publisher","first-page":"1176","DOI":"10.1021\/ct050123f","volume":"1","year":"2005","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c64","doi-asserted-by":"publisher","first-page":"1370","DOI":"10.1021\/ct6001169","volume":"2","year":"2006","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c65","doi-asserted-by":"publisher","first-page":"5086","DOI":"10.1021\/ct400698y","volume":"9","year":"2013","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c66","doi-asserted-by":"publisher","first-page":"13728","DOI":"10.1021\/jp036236h","volume":"107","year":"2003","journal-title":"J.\u00a0Phys. Chem. B"},{"key":"2024071510214127200_c67","doi-asserted-by":"publisher","first-page":"825","DOI":"10.1007\/s00214-010-0816-5","volume":"128","year":"2011","journal-title":"Theor. Chem. Acc."},{"key":"2024071510214127200_c68","doi-asserted-by":"publisher","first-page":"6010","DOI":"10.1021\/acs.jctc.7b00621","volume":"13","year":"2017","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c69","doi-asserted-by":"publisher","first-page":"4351","DOI":"10.1021\/jp004348s","volume":"105","year":"2001","journal-title":"J.\u00a0Phys. Chem. A"},{"key":"2024071510214127200_c70","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1007\/978-3-319-21626-3","volume-title":"Quantum Modeling of Complex Molecular Systems","author":"Rivail","year":"2015"},{"key":"2024071510214127200_c71","doi-asserted-by":"publisher","first-page":"1170","DOI":"10.1002\/jcc.540160911","volume":"16","year":"1995","journal-title":"J.\u00a0Comput. Chem."},{"key":"2024071510214127200_c72","doi-asserted-by":"publisher","first-page":"1102","DOI":"10.1021\/acs.jctc.6b00727","volume":"13","year":"2017","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c73","doi-asserted-by":"publisher","first-page":"2466","DOI":"10.3390\/molecules23102466","volume":"23","year":"2018","journal-title":"Molecules"},{"key":"2024071510214127200_c74","doi-asserted-by":"publisher","first-page":"5678","DOI":"10.1021\/cr5004419","volume":"115","year":"2015","journal-title":"Chem. Rev."},{"key":"2024071510214127200_c75","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1002\/jcc.540160105","volume":"16","year":"1995","journal-title":"J.\u00a0Comput. Chem."},{"key":"2024071510214127200_c76","doi-asserted-by":"publisher","first-page":"422","DOI":"10.1002\/wcms.1180","volume":"4","year":"2014","journal-title":"WIREs Comput. Mol. Sci."},{"key":"2024071510214127200_c77","doi-asserted-by":"publisher","first-page":"11653","DOI":"10.1021\/jp507967z","volume":"118","year":"2014","journal-title":"J.\u00a0Phys. Chem. A"},{"key":"2024071510214127200_c78","doi-asserted-by":"publisher","first-page":"044103","DOI":"10.1063\/1.4926652","volume":"143","year":"2015","journal-title":"J.\u00a0Chem. Phys."},{"key":"2024071510214127200_c79","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1007\/s00214-016-1923-8","volume":"135","year":"2016","journal-title":"Theor. Chem. Acc."},{"key":"2024071510214127200_c80","doi-asserted-by":"publisher","first-page":"2500","DOI":"10.3390\/molecules23102500","volume":"23","year":"2018","journal-title":"Molecules"},{"key":"2024071510214127200_c81","doi-asserted-by":"publisher","first-page":"116447","DOI":"10.1016\/j.ces.2021.116447","volume":"234","year":"2021","journal-title":"Chem. Eng. Sci."},{"key":"2024071510214127200_c82","doi-asserted-by":"publisher","first-page":"3561","DOI":"10.1021\/acs.jctc.6b00269","volume":"12","year":"2016","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c83","doi-asserted-by":"publisher","first-page":"1019","DOI":"10.1002\/jcc.20857","volume":"29","year":"2008","journal-title":"J.\u00a0Comput. Chem."},{"key":"2024071510214127200_c84","doi-asserted-by":"publisher","first-page":"17715","DOI":"10.1021\/jp0517192","volume":"109","year":"2005","journal-title":"J.\u00a0Phys. Chem. B"},{"key":"2024071510214127200_c85","doi-asserted-by":"publisher","first-page":"021101","DOI":"10.1063\/5.0133646","volume":"158","year":"2023","journal-title":"J.\u00a0Chem. Phys."},{"key":"2024071510214127200_c86","doi-asserted-by":"publisher","first-page":"2611","DOI":"10.1021\/acs.jctc.6b00198","volume":"12","year":"2016","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c87","doi-asserted-by":"publisher","first-page":"2","DOI":"10.1021\/ct049941i","volume":"1","year":"2005","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c88","doi-asserted-by":"publisher","first-page":"244108","DOI":"10.1063\/1.4850655","volume":"139","year":"2013","journal-title":"J.\u00a0Chem. Phys."},{"key":"2024071510214127200_c89","doi-asserted-by":"publisher","first-page":"059901","DOI":"10.1063\/1.4907623","volume":"142","year":"2015","journal-title":"J.\u00a0Chem. Phys."},{"key":"2024071510214127200_c90","doi-asserted-by":"publisher","first-page":"144115","DOI":"10.1063\/1.5089673","volume":"150","year":"2019","journal-title":"J.\u00a0Chem. Phys."},{"key":"2024071510214127200_c91","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1016\/j.chemphys.2015.08.021","volume":"461","year":"2015","journal-title":"Chem. Phys."},{"key":"2024071510214127200_c92","doi-asserted-by":"publisher","first-page":"174105","DOI":"10.1063\/5.0087386","volume":"156","year":"2022","journal-title":"J.\u00a0Chem. Phys."},{"key":"2024071510214127200_c93","first-page":"105","volume-title":"Methods in Enzymology","year":"2016"},{"key":"2024071510214127200_c94","doi-asserted-by":"publisher","first-page":"134","DOI":"10.1021\/ct400724d","volume":"10","year":"2014","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c95","doi-asserted-by":"publisher","first-page":"174111","DOI":"10.1063\/1.4934880","volume":"143","year":"2015","journal-title":"J.\u00a0Chem. Phys."},{"key":"2024071510214127200_c96","doi-asserted-by":"publisher","first-page":"234503","DOI":"10.1063\/1.1931667","volume":"122","year":"2005","journal-title":"J.\u00a0Chem. Phys."},{"key":"2024071510214127200_c97","doi-asserted-by":"publisher","first-page":"1250","DOI":"10.1002\/ijch.201400036","volume":"54","year":"2014","journal-title":"Isr. J. Chem."},{"key":"2024071510214127200_c98","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1007\/978-3-540-38085-6","volume-title":"Atomistic Approaches in Modern Biology","author":"Reiher","year":"2007"},{"key":"2024071510214127200_c99","doi-asserted-by":"publisher","first-page":"227","DOI":"10.1016\/0022-2836(76)90311-9","volume":"103","year":"1976","journal-title":"J.\u00a0Mol. Biol."},{"key":"2024071510214127200_c100","doi-asserted-by":"publisher","first-page":"718","DOI":"10.1002\/jcc.540070604","volume":"7","year":"1986","journal-title":"J.\u00a0Comput. Chem."},{"key":"2024071510214127200_c101","doi-asserted-by":"publisher","first-page":"351","DOI":"10.1038\/nmeth.4638","volume":"15","year":"2018","journal-title":"Nat. Methods"},{"key":"2024071510214127200_c102","doi-asserted-by":"publisher","first-page":"700","DOI":"10.1002\/jcc.540110605","volume":"11","year":"1990","journal-title":"J.\u00a0Comput. Chem."},{"key":"2024071510214127200_c103","doi-asserted-by":"publisher","first-page":"5849","DOI":"10.1021\/acs.jcim.2c01239","volume":"62","year":"2022","journal-title":"J.\u00a0Chem. Inf. Model."},{"key":"2024071510214127200_c104","doi-asserted-by":"publisher","first-page":"1689","DOI":"10.1002\/jcc.20297","volume":"26","year":"2005","journal-title":"J.\u00a0Comput. Chem."},{"key":"2024071510214127200_c105","doi-asserted-by":"publisher","first-page":"5655","DOI":"10.1021\/jp070071l","volume":"111","year":"2007","journal-title":"J.\u00a0Phys. Chem. A"},{"key":"2024071510214127200_c106","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/s0166-1280(98)00475-8","volume":"461\u2013462","year":"1999","journal-title":"J.\u00a0Mol. Struct.: THEOCHEM"},{"key":"2024071510214127200_c107","doi-asserted-by":"publisher","first-page":"1545","DOI":"10.1002\/jcc.21287","volume":"30","year":"2009","journal-title":"J.\u00a0Comput. Chem."},{"key":"2024071510214127200_c108","doi-asserted-by":"publisher","first-page":"1668","DOI":"10.1002\/jcc.20290","volume":"26","year":"2005","journal-title":"J.\u00a0Comput. Chem."},{"key":"2024071510214127200_c109","doi-asserted-by":"publisher","first-page":"e26343","DOI":"10.1002\/qua.26343","volume":"120","year":"2020","journal-title":"Int. J. Quantum Chem."},{"key":"2024071510214127200_c110","doi-asserted-by":"publisher","first-page":"1442","DOI":"10.1002\/1096-987x(200012)21:16&lt;1442::aid-jcc3&gt;3.0.co;2-o","volume":"21","year":"2000","journal-title":"J.\u00a0Comput. Chem."},{"key":"2024071510214127200_c111","doi-asserted-by":"publisher","first-page":"7877","DOI":"10.1021\/jp9717296","volume":"101","year":"1997","journal-title":"J.\u00a0Phys. Chem. B"},{"key":"2024071510214127200_c112","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1007\/s002140050391","volume":"100","year":"1998","journal-title":"Theor. Chem. Acc.: Theory, Comput., Model. (Theor. Chim. Acta)"},{"key":"2024071510214127200_c113","doi-asserted-by":"publisher","first-page":"569","DOI":"10.1021\/jp0029109","volume":"105","year":"2001","journal-title":"J.\u00a0Phys. Chem. B"},{"key":"2024071510214127200_c114","doi-asserted-by":"publisher","first-page":"1151","DOI":"10.1021\/ct800092p","volume":"4","year":"2008","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c115","doi-asserted-by":"publisher","first-page":"2328","DOI":"10.1002\/jcc.21810","volume":"32","year":"2011","journal-title":"J.\u00a0Comput. Chem."},{"key":"2024071510214127200_c116","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1002\/jcc.23444","volume":"35","year":"2014","journal-title":"J.\u00a0Comput. Chem."},{"key":"2024071510214127200_c117","doi-asserted-by":"publisher","first-page":"1125","DOI":"10.1002\/jcc.24318","volume":"37","year":"2016","journal-title":"J.\u00a0Comput. Chem."},{"key":"2024071510214127200_c118","doi-asserted-by":"publisher","first-page":"799","DOI":"10.1002\/jcc.25146","volume":"39","year":"2018","journal-title":"J.\u00a0Comput. Chem."},{"key":"2024071510214127200_c119","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1039\/9781839164668-00001","volume-title":"Theoretical and Computational Chemistry","author":"Salahub","year":"2022"},{"key":"2024071510214127200_c120","doi-asserted-by":"publisher","first-page":"044801","DOI":"10.1063\/5.0130886","volume":"158","year":"2023","journal-title":"J.\u00a0Chem. Phys."},{"key":"2024071510214127200_c121","doi-asserted-by":"publisher","first-page":"5357","DOI":"10.1021\/acs.inorgchem.2c03967","volume":"62","year":"2023","journal-title":"Inorg. Chem."},{"key":"2024071510214127200_c122","doi-asserted-by":"publisher","first-page":"1406","DOI":"10.1021\/acs.jcim.2c01620","volume":"63","year":"2023","journal-title":"J.\u00a0Chem. Inf. Model."},{"key":"2024071510214127200_c123","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1002\/jcc.24513","volume":"38","year":"2017","journal-title":"J.\u00a0Comput. Chem."},{"key":"2024071510214127200_c124","doi-asserted-by":"publisher","first-page":"184","DOI":"10.1080\/00268976.2014.952696","volume":"113","year":"2015","journal-title":"Mol. Phys."},{"key":"2024071510214127200_c125","doi-asserted-by":"publisher","first-page":"092503","DOI":"10.1063\/5.0182685","volume":"160","year":"2024","journal-title":"J.\u00a0Chem. Phys."},{"key":"2024071510214127200_c126","doi-asserted-by":"publisher","first-page":"70","DOI":"10.3389\/fchem.2018.00070","volume":"6","year":"2018","journal-title":"Front. Chem."},{"key":"2024071510214127200_c127","doi-asserted-by":"publisher","first-page":"5105","DOI":"10.1021\/jp983678y","volume":"103","year":"1999","journal-title":"J.\u00a0Phys. Chem. A"},{"key":"2024071510214127200_c128","doi-asserted-by":"publisher","first-page":"3245","DOI":"10.1021\/jp982600e","volume":"103","year":"1999","journal-title":"J.\u00a0Phys. Chem. A"},{"key":"2024071510214127200_c129","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1016\/j.cpc.2015.04.024","volume":"195","year":"2015","journal-title":"Comput. Phys. Commun."},{"key":"2024071510214127200_c130","doi-asserted-by":"publisher","first-page":"1088","DOI":"10.1002\/1096-987x(200009)21:12&lt;1088::aid-jcc5&gt;3.3.co;2-#","volume":"21","year":"2000","journal-title":"J.\u00a0Comput. Chem."},{"key":"2024071510214127200_c131","doi-asserted-by":"publisher","first-page":"704","DOI":"10.1002\/jcc.540150704","volume":"15","year":"1994","journal-title":"J.\u00a0Comput. Chem."},{"key":"2024071510214127200_c132","doi-asserted-by":"publisher","first-page":"1653","DOI":"10.3390\/molecules24091653","volume":"24","year":"2019","journal-title":"Molecules"},{"key":"2024071510214127200_c133","doi-asserted-by":"publisher","first-page":"260","DOI":"10.1016\/s0010-4655(00)00065-5","volume":"128","year":"2000","journal-title":"Comput. Phys. Commun."},{"key":"2024071510214127200_c134","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.cplett.2012.01.008","volume":"530","year":"2012","journal-title":"Chem. Phys. Lett."},{"key":"2024071510214127200_c135","doi-asserted-by":"publisher","first-page":"2816","DOI":"10.1002\/jcc.23435","volume":"34","year":"2013","journal-title":"J.\u00a0Comput. Chem."},{"key":"2024071510214127200_c136","doi-asserted-by":"publisher","first-page":"1978","DOI":"10.1002\/jcc.24029","volume":"36","year":"2015","journal-title":"J.\u00a0Comput. Chem."},{"key":"2024071510214127200_c137","doi-asserted-by":"publisher","first-page":"931","DOI":"10.1002\/jcc.1056","volume":"22","year":"2001","journal-title":"J.\u00a0Comput. Chem."},{"key":"2024071510214127200_c138","doi-asserted-by":"publisher","first-page":"1485","DOI":"10.1002\/jcc.20587","volume":"28","year":"2007","journal-title":"J.\u00a0Comput. Chem."},{"key":"2024071510214127200_c139","doi-asserted-by":"publisher","first-page":"932","DOI":"10.1002\/jcc.21678","volume":"32","year":"2011","journal-title":"J.\u00a0Comput. Chem."},{"key":"2024071510214127200_c140","doi-asserted-by":"publisher","first-page":"2108","DOI":"10.1002\/jcc.23047","volume":"33","year":"2012","journal-title":"J.\u00a0Comput. Chem."},{"key":"2024071510214127200_c141","doi-asserted-by":"publisher","first-page":"13","DOI":"10.2533\/000942902777680865","volume":"56","year":"2002","journal-title":"Chimia"},{"key":"2024071510214127200_c142","doi-asserted-by":"publisher","first-page":"1240","DOI":"10.1002\/jcc.10283","volume":"24","year":"2003","journal-title":"J.\u00a0Comput. Chem."},{"key":"2024071510214127200_c143","doi-asserted-by":"publisher","first-page":"4780","DOI":"10.3390\/molecules20034780","volume":"20","year":"2015","journal-title":"Molecules"},{"key":"2024071510214127200_c144","doi-asserted-by":"publisher","first-page":"1657","DOI":"10.1002\/jcc.24379","volume":"37","year":"2016","journal-title":"J.\u00a0Comput. Chem."},{"key":"2024071510214127200_c145","doi-asserted-by":"publisher","first-page":"132","DOI":"10.1007\/s00214-015-1734-3","volume":"134","year":"2015","journal-title":"Theor. Chem. Acc."},{"key":"2024071510214127200_c146","doi-asserted-by":"publisher","first-page":"164114","DOI":"10.1063\/1.2064907","volume":"123","year":"2005","journal-title":"J.\u00a0Chem. Phys."},{"key":"2024071510214127200_c147","doi-asserted-by":"publisher","first-page":"10663","DOI":"10.1021\/jp026464w","volume":"106","year":"2002","journal-title":"J.\u00a0Phys. Chem. A"},{"key":"2024071510214127200_c148","doi-asserted-by":"publisher","first-page":"3462","DOI":"10.1021\/jp982115j","volume":"103","year":"1999","journal-title":"J.\u00a0Phys. Chem. A"},{"key":"2024071510214127200_c149","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1007\/bf00402823","volume":"10","year":"1996","journal-title":"J.\u00a0Comput.-Aided Mol. Des."},{"key":"2024071510214127200_c150","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1002\/1097-461x(2001)81:5&lt;335::aid-qua1003&gt;3.0.co;2-q","volume":"81","year":"2001","journal-title":"Int. J. Quantum Chem."},{"key":"2024071510214127200_c151","doi-asserted-by":"publisher","first-page":"1470","DOI":"10.1002\/1096-987x(200012)21:16&lt;1470::aid-jcc5&gt;3.0.co;2-l","volume":"21","year":"2000","journal-title":"J.\u00a0Comput. Chem."},{"key":"2024071510214127200_c152","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/s0166-1280(03)00285-9","volume":"632","year":"2003","journal-title":"J.\u00a0Mol. Struct.: THEOCHEM"},{"key":"2024071510214127200_c153","doi-asserted-by":"publisher","first-page":"165","DOI":"10.1039\/b314768a","volume":"127","year":"2004","journal-title":"Faraday Disc."},{"key":"2024071510214127200_c154","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1002\/wcms.1163","volume":"4","year":"2014","journal-title":"WIREs Comput. Mol. Sci."},{"key":"2024071510214127200_c155","doi-asserted-by":"publisher","first-page":"1317","DOI":"10.1021\/acs.jctc.8b01036","volume":"15","year":"2019","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c156","doi-asserted-by":"publisher","first-page":"21816","DOI":"10.1039\/d3cp00648d","volume":"25","year":"2023","journal-title":"Phys. Chem. Chem. Phys."},{"key":"2024071510214127200_c157","doi-asserted-by":"publisher","first-page":"3991","DOI":"10.1021\/jp0446332","volume":"109","year":"2005","journal-title":"J.\u00a0Phys. Chem. A"},{"key":"2024071510214127200_c158","doi-asserted-by":"publisher","first-page":"108987","DOI":"10.1016\/j.cpc.2023.108987","volume":"295","year":"2024","journal-title":"Comput. Phys. Commun."},{"key":"2024071510214127200_c159","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1007\/s00214-007-0275-9","volume":"118","year":"2007","journal-title":"Theor. Chem. Acc."},{"key":"2024071510214127200_c160","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1007\/s10820-006-9011-3","volume":"13","year":"2006","journal-title":"J.\u00a0Comput.-Aided Mol. Des."},{"key":"2024071510214127200_c161","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1016\/j.cpc.2007.01.009","volume":"177","year":"2007","journal-title":"Comput. Phys. Commun."},{"key":"2024071510214127200_c162","first-page":"1","volume-title":"Combined Quantum Mechanical and Molecular Mechanical Modelling of Biomolecular Interactions","year":"2015"},{"key":"2024071510214127200_c163","doi-asserted-by":"publisher","first-page":"1019","DOI":"10.1002\/jcc.24295","volume":"37","year":"2016","journal-title":"J.\u00a0Comput. Chem."},{"key":"2024071510214127200_c164","doi-asserted-by":"publisher","first-page":"1230","DOI":"10.1002\/jcc.24312","volume":"37","year":"2016","journal-title":"J.\u00a0Comput. Chem."},{"key":"2024071510214127200_c165","doi-asserted-by":"publisher","first-page":"3056","DOI":"10.1021\/acs.jctc.9b00028","volume":"15","year":"2019","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c166","doi-asserted-by":"publisher","first-page":"e1644","DOI":"10.1002\/wcms.1644","volume":"13","year":"2023","journal-title":"WIREs Comput. Mol. Sci."},{"key":"2024071510214127200_c167","doi-asserted-by":"publisher","first-page":"4362","DOI":"10.1021\/acs.jctc.9b00182","volume":"15","year":"2019","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c168","doi-asserted-by":"publisher","first-page":"447","DOI":"10.1002\/jcc.26465","volume":"42","year":"2021","journal-title":"J.\u00a0Comput. Chem."},{"key":"2024071510214127200_c169","doi-asserted-by":"publisher","first-page":"3810","DOI":"10.1021\/acs.jctc.9b00093","volume":"15","year":"2019","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c170","doi-asserted-by":"crossref","unstructured":"A.\n            Antal\u00edk\n          , A.Levy, S.Kvedaravi\u010di\u016bt\u0117, S. K.Johnson, D.Carrasco-Busturia, B.Raghavan, F.Mouvet, A.Acocella, S.Das, V.Gavini, D.Mandelli, E.Ippoliti, S.Meloni, P.Carloni, U.Rothlisberger, and J. M. H.Olsen, \u201cMiMiC: A high-performance framework for multiscale molecular dynamics simulations,\u201d [physics] arXiv:2403.19035 (2024).","DOI":"10.1063\/5.0211053"},{"key":"2024071510214127200_c171","doi-asserted-by":"publisher","first-page":"107688","DOI":"10.1016\/j.cpc.2020.107688","volume":"261","year":"2021","journal-title":"Comput. Phys. Commun."},{"key":"2024071510214127200_c172","doi-asserted-by":"publisher","first-page":"180901","DOI":"10.1063\/5.0175165","volume":"159","year":"2023","journal-title":"J.\u00a0Chem. Phys."},{"key":"2024071510214127200_c173","doi-asserted-by":"publisher","first-page":"1787","DOI":"10.1021\/jp980314x","volume":"102","year":"1998","journal-title":"J.\u00a0Phys. Chem. B"},{"key":"2024071510214127200_c174","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1007\/s00214-002-0418-y","volume":"109","year":"2003","journal-title":"Theor. Chem. Acc.: Theory, Comput., Model. (Theor. Chim. Acta)"},{"key":"2024071510214127200_c175","doi-asserted-by":"publisher","first-page":"815","DOI":"10.1021\/ct050289g","volume":"2","year":"2006","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c176","doi-asserted-by":"publisher","first-page":"024117","DOI":"10.1063\/5.0012901","volume":"153","year":"2020","journal-title":"J.\u00a0Chem. Phys."},{"key":"2024071510214127200_c177","first-page":"273002","volume":"29","year":"2017","journal-title":"J.\u00a0Phys.: Condens. Matter"},{"key":"2024071510214127200_c178","doi-asserted-by":"publisher","first-page":"556","DOI":"10.1002\/wcms.93","volume":"2","year":"2012","journal-title":"WIREs Comput. Mol. Sci."},{"key":"2024071510214127200_c179","doi-asserted-by":"publisher","first-page":"3185","DOI":"10.1021\/acs.jctc.7b00174","volume":"13","year":"2017","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c180","doi-asserted-by":"publisher","first-page":"e1340","DOI":"10.1002\/wcms.1340","volume":"8","year":"2017","journal-title":"WIREs Comput. Mol. Sci."},{"key":"2024071510214127200_c181","doi-asserted-by":"publisher","first-page":"e1005659","DOI":"10.1371\/journal.pcbi.1005659","volume":"13","year":"2017","journal-title":"PLoS Comput. Biol."},{"key":"2024071510214127200_c182","doi-asserted-by":"publisher","first-page":"3504","DOI":"10.1021\/acs.jctc.8b00286","volume":"14","year":"2018","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c183","doi-asserted-by":"publisher","first-page":"e1663","DOI":"10.1002\/wcms.1688","volume":"13","year":"2023","journal-title":"WIREs Comput. Mol. Sci."},{"key":"2024071510214127200_c184","doi-asserted-by":"publisher","first-page":"e1610","DOI":"10.1002\/wcms.1610","volume":"12","year":"2022","journal-title":"WIREs Comput. Mol. Sci."},{"key":"2024071510214127200_c185","doi-asserted-by":"publisher","first-page":"7056","DOI":"10.1021\/acs.jctc.3c00419","volume":"19","year":"2023","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c186","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1109\/mcse.2010.27","volume":"12","year":"2010","journal-title":"Comput. Sci. Eng."},{"key":"2024071510214127200_c187","doi-asserted-by":"publisher","first-page":"184108","DOI":"10.1063\/5.0006002","volume":"152","year":"2020","journal-title":"J.\u00a0Chem. Phys."},{"key":"2024071510214127200_c188","doi-asserted-by":"publisher","first-page":"461","DOI":"10.1021\/ct300857j","volume":"9","year":"2013","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c189","doi-asserted-by":"publisher","first-page":"8577","DOI":"10.1063\/1.470117","volume":"103","year":"1995","journal-title":"J.\u00a0Chem. Phys."},{"key":"2024071510214127200_c190","doi-asserted-by":"publisher","first-page":"89","DOI":"10.3389\/fchem.2018.00089","volume":"6","year":"2018","journal-title":"Front. Chem."},{"key":"2024071510214127200_c191","doi-asserted-by":"publisher","first-page":"6374","DOI":"10.1021\/j100017a017","volume":"99","year":"1995","journal-title":"J.\u00a0Phys. Chem."},{"key":"2024071510214127200_c192","doi-asserted-by":"publisher","first-page":"14492","DOI":"10.1021\/jp960690m","volume":"100","year":"1996","journal-title":"J.\u00a0Phys. Chem."},{"key":"2024071510214127200_c193","doi-asserted-by":"publisher","first-page":"835","DOI":"10.1080\/00268979709482774","volume":"91","year":"1997","journal-title":"Mol. Phys."},{"key":"2024071510214127200_c194","doi-asserted-by":"publisher","first-page":"1061","DOI":"10.1002\/(sici)1096-987x(199706)18:8&lt;1061::aid-jcc10&gt;3.3.co;2-7","volume":"18","year":"1997","journal-title":"J.\u00a0Comput. Chem."},{"key":"2024071510214127200_c195","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1021\/ct050218h","volume":"2","year":"2006","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c196","doi-asserted-by":"publisher","first-page":"1838","DOI":"10.1021\/ct9001366","volume":"5","year":"2009","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c197","doi-asserted-by":"publisher","first-page":"2954","DOI":"10.1021\/acs.jctc.7b00016","volume":"13","year":"2017","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c198","doi-asserted-by":"publisher","first-page":"074103","DOI":"10.1063\/1.5080384","volume":"150","year":"2019","journal-title":"J.\u00a0Chem. Phys."},{"key":"2024071510214127200_c199","doi-asserted-by":"publisher","first-page":"2233","DOI":"10.1021\/acs.jctc.8b01149","volume":"15","year":"2019","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c200","doi-asserted-by":"publisher","first-page":"2111","DOI":"10.1021\/acs.jctc.3c01018","volume":"20","year":"2024","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c201","doi-asserted-by":"publisher","first-page":"7462","DOI":"10.1021\/acs.jctc.0c00932","volume":"16","year":"2020","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c202","doi-asserted-by":"publisher","first-page":"026501","DOI":"10.1088\/0034-4885\/72\/2\/026501","volume":"72","year":"2009","journal-title":"Rep. Prog. Phys."},{"key":"2024071510214127200_c203","doi-asserted-by":"publisher","first-page":"2228","DOI":"10.1021\/jp026742r","volume":"107","year":"2003","journal-title":"J.\u00a0Phys. Chem. B"},{"key":"2024071510214127200_c204","doi-asserted-by":"publisher","first-page":"498","DOI":"10.1116\/1.571046","volume":"19","year":"1981","journal-title":"JournJ. Vac. Sci. Technol."},{"key":"2024071510214127200_c205","first-page":"119","volume-title":"Methods in Enzymology","year":"2016"},{"key":"2024071510214127200_c206","doi-asserted-by":"publisher","first-page":"4714","DOI":"10.1021\/jp9809890","volume":"102","year":"1998","journal-title":"J.\u00a0Phys. Chem. A"},{"key":"2024071510214127200_c207","doi-asserted-by":"publisher","first-page":"1468","DOI":"10.1002\/(sici)1096-987x(19991115)20:14&lt;1468::aid-jcc2&gt;3.0.co;2-0","volume":"20","year":"1999","journal-title":"J.\u00a0Comput. Chem."},{"key":"2024071510214127200_c208","doi-asserted-by":"publisher","first-page":"269","DOI":"10.1002\/jcc.540150303","volume":"15","year":"1994","journal-title":"J.\u00a0Comput. Chem."},{"key":"2024071510214127200_c209","doi-asserted-by":"publisher","first-page":"6656","DOI":"10.1021\/jp000887l","volume":"104","year":"2000","journal-title":"J.\u00a0Phys. Chem. A"},{"key":"2024071510214127200_c210","doi-asserted-by":"publisher","first-page":"632","DOI":"10.1021\/jp036755k","volume":"108","year":"2004","journal-title":"J.\u00a0Phys. Chem. A"},{"key":"2024071510214127200_c211","doi-asserted-by":"publisher","first-page":"596","DOI":"10.1021\/ar300278j","volume":"46","year":"2013","journal-title":"Acc. Chem. Res."},{"key":"2024071510214127200_c212","doi-asserted-by":"publisher","first-page":"204102","DOI":"10.1063\/1.2801988","volume":"127","year":"2007","journal-title":"J.\u00a0Chem. Phys."},{"key":"2024071510214127200_c213","doi-asserted-by":"publisher","first-page":"1213","DOI":"10.1021\/jp507983u","volume":"119","year":"2015","journal-title":"J.\u00a0Phys. Chem. B"},{"key":"2024071510214127200_c214","doi-asserted-by":"publisher","first-page":"174","DOI":"10.1007\/s002140000138","article-title":"A new method for modelling spectator chemical groups in ab\u00a0initio calculations: Effective group potentials","volume":"104","year":"2000","journal-title":"Theor. Chem. Acc.: Theory, Comput., Model. (Theor. Chim. Acta)"},{"key":"2024071510214127200_c215","doi-asserted-by":"publisher","first-page":"9578","DOI":"10.1063\/1.1477182","volume":"116","year":"2002","journal-title":"J.\u00a0Chem. Phys."},{"key":"2024071510214127200_c216","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1016\/s0166-1280(03)00287-2","volume":"632","year":"2003","journal-title":"J.\u00a0Mol. Struct.: THEOCHEM"},{"key":"2024071510214127200_c217","doi-asserted-by":"publisher","first-page":"1019","DOI":"10.1002\/qua.20296","volume":"100","year":"2004","journal-title":"Int. J. Quantum Chem."},{"key":"2024071510214127200_c218","doi-asserted-by":"publisher","first-page":"9080","DOI":"10.1063\/1.1689633","volume":"120","year":"2004","journal-title":"J.\u00a0Chem. Phys."},{"key":"2024071510214127200_c219","doi-asserted-by":"publisher","first-page":"3964","DOI":"10.1063\/1.1772354","volume":"121","year":"2004","journal-title":"J.\u00a0Chem. Phys."},{"key":"2024071510214127200_c220","doi-asserted-by":"publisher","first-page":"014113","DOI":"10.1063\/1.1829051","volume":"122","year":"2005","journal-title":"J.\u00a0Chem. Phys."},{"key":"2024071510214127200_c221","doi-asserted-by":"publisher","first-page":"084107","DOI":"10.1063\/1.2173992","volume":"124","year":"2006","journal-title":"J.\u00a0Chem. Phys."},{"key":"2024071510214127200_c222","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1016\/j.cplett.2008.01.073","volume":"454","year":"2008","journal-title":"Chem. Phys. Lett."},{"key":"2024071510214127200_c223","doi-asserted-by":"publisher","first-page":"12754","DOI":"10.1021\/jp711830a","volume":"112","year":"2008","journal-title":"J.\u00a0Phys. Chem. A"},{"key":"2024071510214127200_c224","doi-asserted-by":"publisher","first-page":"1946","DOI":"10.1021\/jp710310s","volume":"112","year":"2008","journal-title":"J.\u00a0Phys. Chem. A"},{"key":"2024071510214127200_c225","doi-asserted-by":"publisher","first-page":"1490","DOI":"10.1021\/ct800525u","volume":"5","year":"2009","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c226","doi-asserted-by":"publisher","first-page":"10580","DOI":"10.1021\/jp9536514","volume":"100","year":"1996","journal-title":"J.\u00a0Phys. Chem."},{"key":"2024071510214127200_c227","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1007\/s00214-002-0413-3","volume":"109","year":"2003","journal-title":"Theor. Chem. Acc.: Theory, Comput., Model. (Theor. Chim. Acta)"},{"key":"2024071510214127200_c228","doi-asserted-by":"publisher","first-page":"1929","DOI":"10.1002\/jcc.24032","volume":"36","year":"2015","journal-title":"J.\u00a0Comput. Chem."},{"key":"2024071510214127200_c229","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1016\/0009-2614(90)85396-t","volume":"172","year":"1990","journal-title":"Chem. Phys. Lett."},{"key":"2024071510214127200_c230","doi-asserted-by":"publisher","first-page":"9290","DOI":"10.1021\/jp991771w","volume":"103","year":"1999","journal-title":"J.\u00a0Phys. Chem. A"},{"key":"2024071510214127200_c231","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1016\/j.theochem.2004.05.003","volume":"680","year":"2004","journal-title":"J.\u00a0Mol. Struct.: THEOCHEM"},{"key":"2024071510214127200_c232","doi-asserted-by":"publisher","first-page":"270","DOI":"10.1007\/s00214-003-0522-7","volume":"111","year":"2004","journal-title":"Theor. Chem. Acc."},{"key":"2024071510214127200_c233","doi-asserted-by":"publisher","first-page":"161","DOI":"10.1016\/j.theochem.2005.10.026","volume":"758","year":"2006","journal-title":"J.\u00a0Mol. Struct.: THEOCHEM"},{"key":"2024071510214127200_c234","doi-asserted-by":"publisher","first-page":"354","DOI":"10.1016\/j.cplett.2006.12.084","volume":"435","year":"2007","journal-title":"Chem. Phys. Lett."},{"key":"2024071510214127200_c235","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1063\/1.478083","volume":"110","year":"1999","journal-title":"J.\u00a0Chem. Phys."},{"key":"2024071510214127200_c236","doi-asserted-by":"publisher","first-page":"024114","DOI":"10.1063\/1.1862616","volume":"122","year":"2005","journal-title":"J.\u00a0Chem. Phys."},{"key":"2024071510214127200_c237","doi-asserted-by":"publisher","first-page":"154106","DOI":"10.1063\/1.2994288","volume":"129","year":"2008","journal-title":"J.\u00a0Chem. Phys."},{"key":"2024071510214127200_c238","doi-asserted-by":"publisher","first-page":"359","DOI":"10.1021\/ct900366m","volume":"6","year":"2010","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c239","doi-asserted-by":"publisher","first-page":"1309","DOI":"10.3390\/molecules23061309","volume":"23","year":"2018","journal-title":"Molecules"},{"key":"2024071510214127200_c240","doi-asserted-by":"publisher","first-page":"4208","DOI":"10.1021\/acs.jctc.9b00274","volume":"15","year":"2019","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c241","doi-asserted-by":"publisher","first-page":"2398","DOI":"10.1021\/ct501019y","volume":"11","year":"2015","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c242","doi-asserted-by":"publisher","first-page":"3526","DOI":"10.1021\/ct300091w","volume":"8","year":"2012","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c243","doi-asserted-by":"publisher","first-page":"044120","DOI":"10.1063\/1.4821990","volume":"139","year":"2013","journal-title":"J.\u00a0Chem. Phys."},{"key":"2024071510214127200_c244","doi-asserted-by":"publisher","first-page":"827","DOI":"10.1080\/08927022.2014.938068","volume":"41","year":"2015","journal-title":"Mol. Simul."},{"key":"2024071510214127200_c245","doi-asserted-by":"publisher","first-page":"134119","DOI":"10.1063\/1.5019874","volume":"148","year":"2018","journal-title":"J.\u00a0Chem. Phys."},{"key":"2024071510214127200_c246","doi-asserted-by":"publisher","first-page":"114109","DOI":"10.1063\/1.5089199","volume":"150","year":"2019","journal-title":"J.\u00a0Chem. Phys."},{"key":"2024071510214127200_c247","doi-asserted-by":"publisher","first-page":"224112","DOI":"10.1063\/5.0067855","volume":"155","year":"2021","journal-title":"J.\u00a0Chem. Phys."},{"key":"2024071510214127200_c248","doi-asserted-by":"publisher","first-page":"5863","DOI":"10.1021\/acs.jctc.1c00522","volume":"17","year":"2021","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c249","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1016\/0301-0104(96)00152-8","volume":"211","year":"1996","journal-title":"Chem. Phys."},{"key":"2024071510214127200_c250","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1016\/s0009-2614(02)00210-5","volume":"355","year":"2002","journal-title":"Chem. Phys. Lett."},{"key":"2024071510214127200_c251","doi-asserted-by":"publisher","first-page":"2231","DOI":"10.1021\/jp0673617","volume":"111","year":"2007","journal-title":"J.\u00a0Phys. Chem. B"},{"key":"2024071510214127200_c252","doi-asserted-by":"publisher","first-page":"2212","DOI":"10.1021\/ct900148e","volume":"5","year":"2009","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c253","doi-asserted-by":"publisher","first-page":"646","DOI":"10.1039\/c1cp22600b","volume":"14","year":"2012","journal-title":"Phys. Chem. Chem. Phys."},{"key":"2024071510214127200_c254","doi-asserted-by":"publisher","first-page":"56","DOI":"10.1016\/j.cplett.2011.12.053","volume":"524","year":"2012","journal-title":"Chem. Phys. Lett."},{"key":"2024071510214127200_c255","doi-asserted-by":"publisher","first-page":"3218","DOI":"10.1002\/cphc.201402105","volume":"15","year":"2014","journal-title":"ChemPhysChem"},{"key":"2024071510214127200_c256","doi-asserted-by":"publisher","first-page":"4242","DOI":"10.1021\/ct5005593","volume":"10","year":"2014","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c257","doi-asserted-by":"publisher","first-page":"369","DOI":"10.1002\/wcms.1255","volume":"6","year":"2016","journal-title":"WIREs Comput. Mol. Sci."},{"key":"2024071510214127200_c258","doi-asserted-by":"publisher","first-page":"e1310","DOI":"10.1002\/wcms.1310","volume":"7","year":"2017","journal-title":"WIREs Comput. Mol. Sci."},{"key":"2024071510214127200_c259","doi-asserted-by":"publisher","first-page":"2342","DOI":"10.1021\/acs.jctc.7b00099","volume":"13","year":"2017","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c260","doi-asserted-by":"publisher","first-page":"2170","DOI":"10.3390\/molecules23092170","volume":"23","year":"2018","journal-title":"Molecules"},{"key":"2024071510214127200_c261","doi-asserted-by":"publisher","first-page":"1882","DOI":"10.3390\/molecules23081882","volume":"23","year":"2018","journal-title":"Molecules"},{"key":"2024071510214127200_c262","doi-asserted-by":"publisher","first-page":"3917","DOI":"10.1021\/acs.jctc.9b00180","volume":"15","year":"2019","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c263","doi-asserted-by":"publisher","first-page":"1318","DOI":"10.1021\/acs.jctc.0c01149","volume":"17","year":"2021","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c264","doi-asserted-by":"publisher","first-page":"3625","DOI":"10.1021\/ct2005209","volume":"7","year":"2011","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c265","doi-asserted-by":"publisher","first-page":"4765","DOI":"10.1021\/ct500553x","volume":"10","year":"2014","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c266","doi-asserted-by":"publisher","first-page":"e25336","DOI":"10.1002\/qua.25336","volume":"117","year":"2017","journal-title":"Int J. Quantum Chem."},{"key":"2024071510214127200_c267","doi-asserted-by":"publisher","first-page":"3441","DOI":"10.1021\/acs.jctc.6b00205","volume":"12","year":"2016","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c268","doi-asserted-by":"publisher","first-page":"2429","DOI":"10.1021\/acs.jctc.5b00142","volume":"11","year":"2015","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c269","doi-asserted-by":"publisher","first-page":"351","DOI":"10.1016\/j.cma.2019.04.020","volume":"354","year":"2019","journal-title":"Comput. Methods Appl. Mech. Eng."},{"key":"2024071510214127200_c270","doi-asserted-by":"publisher","first-page":"19307","DOI":"10.1039\/d0cp03034a","volume":"22","year":"2020","journal-title":"Phys. Chem. Chem. Phys."},{"key":"2024071510214127200_c271","doi-asserted-by":"publisher","first-page":"17987","DOI":"10.1039\/d0cp02855j","volume":"22","year":"2020","journal-title":"Phys. Chem. Chem. Phys."},{"key":"2024071510214127200_c272","doi-asserted-by":"publisher","first-page":"5456","DOI":"10.1021\/acs.jctc.1c00556","volume":"17","year":"2021","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c273","doi-asserted-by":"publisher","first-page":"3417","DOI":"10.1039\/d0cp05149g","volume":"23","year":"2021","journal-title":"Phys. Chem. Chem. Phys."},{"key":"2024071510214127200_c274","doi-asserted-by":"publisher","first-page":"256","DOI":"10.1016\/j.mspro.2014.07.032","volume":"6","year":"2014","journal-title":"Procedia Mater. Sci."},{"key":"2024071510214127200_c275","doi-asserted-by":"publisher","first-page":"5567","DOI":"10.1021\/ct4005596","volume":"9","year":"2013","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c276","volume-title":"Design Patterns: Elements of Reusable Object-Oriented Software","year":"1995"},{"key":"2024071510214127200_c277","volume-title":"Applying UML and Patterns: An Introduction to Object-Oriented Analysis and Design","year":"1998"},{"key":"2024071510214127200_c278","first-page":"597","volume":"1","year":"2000","journal-title":"Object Mentor"},{"key":"2024071510214127200_c279","doi-asserted-by":"publisher","first-page":"670","DOI":"10.1038\/s41592-019-0506-8","volume":"16","year":"2019","journal-title":"Nat. Methods"},{"key":"2024071510214127200_c280","doi-asserted-by":"publisher","first-page":"952","DOI":"10.1002\/jcc.540130805","volume":"13","year":"1992","journal-title":"J.\u00a0Comput. Chem."},{"key":"2024071510214127200_c281","doi-asserted-by":"publisher","first-page":"2490","DOI":"10.1021\/acs.jpclett.6b00893","volume":"7","year":"2016","journal-title":"J.\u00a0Phys. Chem. Lett."},{"key":"2024071510214127200_c282","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","volume":"14","year":"1996","journal-title":"J.\u00a0Mol. Graphics"},{"key":"2024071510214127200_c283","doi-asserted-by":"publisher","first-page":"5313","DOI":"10.1021\/ct400704a","volume":"9","year":"2013","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c284","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1098\/rsif.2008.0243.focus","volume":"5","year":"2008","journal-title":"J.\u00a0R. Soc., Interface"},{"key":"2024071510214127200_c285","doi-asserted-by":"publisher","first-page":"6467","DOI":"10.1021\/jp037992q","volume":"108","year":"2004","journal-title":"J.\u00a0Phys. Chem. B"},{"key":"2024071510214127200_c286","doi-asserted-by":"publisher","first-page":"386","DOI":"10.1002\/(sici)1096-987x(199603)17:4&lt;386::aid-jcc1&gt;3.0.co;2-q","volume":"17","year":"1996","journal-title":"J.\u00a0Comput. Chem."},{"key":"2024071510214127200_c287","doi-asserted-by":"publisher","first-page":"2868","DOI":"10.1021\/ct300331f","volume":"8","year":"2012","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c288","doi-asserted-by":"publisher","first-page":"3902","DOI":"10.1021\/ct3001848","volume":"8","year":"2012","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024071510214127200_c289","doi-asserted-by":"publisher","first-page":"19489","DOI":"10.1021\/acs.jpcc.3c03855","volume":"127","year":"2023","journal-title":"J.\u00a0Phys. Chem. C"},{"key":"2024071510214127200_c290"},{"key":"2024071510214127200_c291","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1002\/qua.560160825","volume":"16","year":"2009","journal-title":"Int. J. Quantum Chem."},{"key":"2024071510214127200_c292","doi-asserted-by":"publisher","first-page":"5612","DOI":"10.1063\/1.464906","volume":"98","year":"1993","journal-title":"J.\u00a0Chem. Phys."},{"key":"2024071510214127200_c293","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1016\/0009-2614(94)00199-5","volume":"220","year":"1994","journal-title":"Chem. Phys. Lett."},{"key":"2024071510214127200_c294","doi-asserted-by":"publisher","first-page":"8894","DOI":"10.1063\/1.468081","volume":"101","year":"1994","journal-title":"J.\u00a0Chem. Phys."}],"container-title":["The Journal of Chemical Physics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.aip.org\/aip\/jcp\/article-pdf\/doi\/10.1063\/5.0219851\/20044077\/034103_1_5.0219851.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.aip.org\/aip\/jcp\/article-pdf\/doi\/10.1063\/5.0219851\/20044077\/034103_1_5.0219851.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,15]],"date-time":"2024-07-15T10:22:59Z","timestamp":1721038979000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.aip.org\/jcp\/article\/161\/3\/034103\/3303335\/PyDFT-QMMM-A-modular-extensible-software-framework"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,7,15]]},"references-count":294,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2024,7,21]]}},"URL":"https:\/\/doi.org\/10.1063\/5.0219851","relation":{},"ISSN":["0021-9606","1089-7690"],"issn-type":[{"value":"0021-9606","type":"print"},{"value":"1089-7690","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,7,21]]},"published":{"date-parts":[[2024,7,15]]},"article-number":"034103"}}