QM/MM Calculations with deMon2k
by
Dennis R. Salahub 1,*, Sergei Yu. Noskov 2, Bogdan Lev 3, Rui Zhang 1, Van Ngo 2, Annick Goursot 4, Patrizia Calaminici 5, Andreas M. Köster 5, Aurelio Alvarez-Ibarra 5, Daniel Mejía-Rodríguez 5, Jan Řezáč 6, Fabien Cailliez 7 and Aurélien De la Lande 7
Dennis R. Salahub 1,*, Sergei Yu. Noskov 2, Bogdan Lev 3, Rui Zhang 1, Van Ngo 2, Annick Goursot 4, Patrizia Calaminici 5, Andreas M. Köster 5, Aurelio Alvarez-Ibarra 5, Daniel Mejía-Rodríguez 5, Jan Řezáč 6, Fabien Cailliez 7 and Aurélien De la Lande 7
1
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
2
Department of Biological Science and CMS—Centre for Molecular Simulation, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
3
School of Applied Sciences and Health Innovation Research Institute, RMIT University, Melbourne, VIC 3001, Australia
4
Institut Charles Gerhardt, UMR 5253 CNRS/UM2/ENSCM/UM1, 8 rue de l'Ecole Normale, Montpellier 34296, France
5
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
6
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
7
Laboratoire de Chimie Physique—CNRS UMR 8000, Université Paris-Sud, Bật. 349, Campus d'Orsay. 15, rue Jean Perrin, Orsay Cedex 91405, France
*
Author to whom correspondence should be addressed.
Academic Editor: James Gauld
Molecules 2015, 20(3), 4780-4812; https://doi.org/10.3390/molecules20034780
Received: 19 September 2014 / Revised: 25 February 2015 / Accepted: 2 March 2015 / Published: 16 March 2015
(This article belongs to the Special Issue Multiscale Chemical Modeling Using Quantum Mechanics/Molecular Mechanics (QM/MM) Methods: Advances and Applications)
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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Keywords:
Quantum Mechanical/Molecular Mechanical; QM/MM; density functional theory; deMon2k software; biomolecular modeling; auxiliary DFT; double asymptotic expansion; constrained DFT
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited
MDPI and ACS Style
Salahub, D.R.; Noskov, S.Y.; Lev, B.; Zhang, R.; Ngo, V.; Goursot, A.; Calaminici, P.; Köster, A.M.; Alvarez-Ibarra, A.; Mejía-Rodríguez, D.; Řezáč, J.; Cailliez, F.; De la Lande, A. QM/MM Calculations with deMon2k. Molecules 2015, 20, 4780-4812.
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