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QM/MM calculations with deMon2k

DR. Salahub, SY. Noskov, B. Lev, R. Zhang, V. Ngo, A. Goursot, P. Calaminici, AM. Köster, A. Alvarez-Ibarra, D. Mejía-Rodríguez, J. Řezáč, F. Cailliez, A. de la Lande,

. 2015 ; 20 (3) : 4780-812. [pub] 20150316

Language English Country Switzerland

Document type Journal Article, Research Support, Non-U.S. Gov't, Review

Persistent link   https://www.medvik.cz/link/bmc16000204

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.

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$a Salahub, Dennis R $u Department of Chemistry, CMS-Centre for Molecular Simulation, IQST-Institute for Quantum Science and Technology and ISEEE-Institute for Sustainable Energy, Environment and Economy, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada. dennis.salahub@ucalgary.ca.
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$a QM/MM calculations with deMon2k / $c DR. Salahub, SY. Noskov, B. Lev, R. Zhang, V. Ngo, A. Goursot, P. Calaminici, AM. Köster, A. Alvarez-Ibarra, D. Mejía-Rodríguez, J. Řezáč, F. Cailliez, A. de la Lande,
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$a 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.
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$a Noskov, Sergei Yu $u Department of Biological Science and CMS-Centre for Molecular Simulation, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada. snoskov@ucalgary.ca.
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$a Lev, Bogdan $u School of Applied Sciences and Health Innovation Research Institute, RMIT University, Melbourne, VIC 3001, Australia. lev.bogdan@gmail.com.
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$a Zhang, Rui $u Department of Chemistry, CMS-Centre for Molecular Simulation, IQST-Institute for Quantum Science and Technology and ISEEE-Institute for Sustainable Energy, Environment and Economy, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada. zhangrui1002@gmail.com.
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$a Ngo, Van $u Department of Biological Science and CMS-Centre for Molecular Simulation, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada. nvan.ucalgary@gmail.com.
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$a Goursot, Annick $u Institut Charles Gerhardt, UMR 5253 CNRS/UM2/ENSCM/UM1, 8 rue de l'Ecole Normale, Montpellier 34296, France. annick.goursot@gmail.com.
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$a Calaminici, Patrizia $u Departamento de Química, CINVESTAV, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, México D.F. 07000, Mexico. pcalamin@cinvestav.mx.
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$a Köster, Andreas M $u Departamento de Química, CINVESTAV, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, México D.F. 07000, Mexico. akoster@cinvestav.mx.
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$a Mejía-Rodríguez, Daniel $u Departamento de Química, CINVESTAV, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, México D.F. 07000, Mexico. dmejia@cinvestav.mx.
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$a Řezáč, Jan $u Institute of Organic Chemistry and Biochemistry and Gilead Science and IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6 166 10, Czech Republic. rezac@uochb.cas.cz.
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$a Cailliez, Fabien $u Laboratoire de Chimie Physique-CNRS UMR 8000, Université Paris-Sud, Bật. 349, Campus d'Orsay. 15, rue Jean Perrin, Orsay Cedex 91405, France. fabien.cailliez@u-psud.fr.
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$a de la Lande, Aurélien $u 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.
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