title: QM/MM calculations with deMon2k.
abstract: The density functional code deMon2k employs a fitted density throughout (Auxiliary Density Functional Theory), which offers a great speed advantage without sacrificing necessary accuracy. Powerful Quantum Mechanical/Molecular Mechanical (QM/MM) approaches are reviewed. Following an overview of the basic features of deMon2k that make it efficient while retaining accuracy, three QM/MM implementations are compared and contrasted. In the first, deMon2k is interfaced with the CHARMM MM code (CHARMM-deMon2k); in the second MM is coded directly within the deMon2k software; and in the third the Chemistry in Ruby (Cuby) wrapper is used to drive the calculations. Cuby is also used in the context of constrained-DFT/MM calculations. Each of these implementations is described briefly; pros and cons are discussed and a few recent applications are described briefly. Applications include solvated ions and biomolecules, polyglutamine peptides important in polyQ neurodegenerative diseases, copper monooxygenases and ultra-rapid electron transfer in cryptochromes.
authors.affiliation: Department of Chemistry, CMS-Centre for Molecular Simulation, IQST-Institute for Quantum Science and Technology and ISEEE-Institute for Sustainable Energy, Environment and Economy, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada. dennis.salahub@ucalgary.ca.
authors.forename: Dennis R
authors.initials: DR
authors.lastname: Salahub
authors.affiliation: Department of Biological Science and CMS-Centre for Molecular Simulation, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada. snoskov@ucalgary.ca.
authors.forename: Sergei Yu
authors.initials: SY
authors.lastname: Noskov
authors.affiliation: School of Applied Sciences and Health Innovation Research Institute, RMIT University, Melbourne, VIC 3001, Australia. lev.bogdan@gmail.com.
authors.forename: Bogdan
authors.initials: B
authors.lastname: Lev
authors.affiliation: Department of Chemistry, CMS-Centre for Molecular Simulation, IQST-Institute for Quantum Science and Technology and ISEEE-Institute for Sustainable Energy, Environment and Economy, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada. zhangrui1002@gmail.com.
authors.forename: Rui
authors.initials: R
authors.lastname: Zhang
authors.affiliation: Department of Biological Science and CMS-Centre for Molecular Simulation, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada. nvan.ucalgary@gmail.com.
authors.forename: Van
authors.initials: V
authors.lastname: Ngo
authors.affiliation: Institut Charles Gerhardt, UMR 5253 CNRS/UM2/ENSCM/UM1, 8 rue de l'Ecole Normale, Montpellier 34296, France. annick.goursot@gmail.com.
authors.forename: Annick
authors.initials: A
authors.lastname: Goursot
authors.affiliation: Departamento de Química, CINVESTAV, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, México D.F. 07000, Mexico. pcalamin@cinvestav.mx.
authors.forename: Patrizia
authors.initials: P
authors.lastname: Calaminici
authors.affiliation: Departamento de Química, CINVESTAV, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, México D.F. 07000, Mexico. akoster@cinvestav.mx.
authors.forename: Andreas M
authors.initials: AM
authors.lastname: Köster
authors.affiliation: Departamento de Química, CINVESTAV, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, México D.F. 07000, Mexico. aalvarezi@cinvestav.mx.
authors.forename: Aurelio
authors.initials: A
authors.lastname: Alvarez-Ibarra
authors.affiliation: Departamento de Química, CINVESTAV, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, México D.F. 07000, Mexico. dmejia@cinvestav.mx.
authors.forename: Daniel
authors.initials: D
authors.lastname: Mejía-Rodríguez
authors.affiliation: Institute of Organic Chemistry and Biochemistry and Gilead Science and IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6 166 10, Czech Republic. rezac@uochb.cas.cz.
authors.forename: Jan
authors.initials: J
authors.lastname: Řezáč
authors.affiliation: Laboratoire de Chimie Physique-CNRS UMR 8000, Université Paris-Sud, Bật. 349, Campus d'Orsay. 15, rue Jean Perrin, Orsay Cedex 91405, France. fabien.cailliez@u-psud.fr.
authors.forename: Fabien
authors.initials: F
authors.lastname: Cailliez
authors.affiliation: Laboratoire de Chimie Physique-CNRS UMR 8000, Université Paris-Sud, Bật. 349, Campus d'Orsay. 15, rue Jean Perrin, Orsay Cedex 91405, France. aurelien.de-la-lande@u-psud.fr.
authors.forename: Aurélien
authors.initials: A
authors.lastname: de la Lande
mesh_terms: D006801:Humans; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*; D011789:Quantum Theory; D012984:Software
chemical_list: D010455:Peptides; C097188:polyglutamine