QM/MM Calculations with deMon2k
AbstractThe 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. View Full-Text
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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.
Salahub DR, Noskov SY, Lev B, Zhang R, Ngo V, Goursot A, Calaminici P, Köster AM, Alvarez-Ibarra A, Mejía-Rodríguez D, Řezáč J, Cailliez F, de la Lande A. QM/MM Calculations with deMon2k. Molecules. 2015; 20(3):4780-4812.Chicago/Turabian Style
Salahub, Dennis R.; Noskov, Sergei Y.; Lev, Bogdan; Zhang, Rui; Ngo, Van; Goursot, Annick; Calaminici, Patrizia; Köster, Andreas M.; Alvarez-Ibarra, Aurelio; Mejía-Rodríguez, Daniel; Řezáč, Jan; Cailliez, Fabien; de la Lande, Aurélien. 2015. "QM/MM Calculations with deMon2k." Molecules 20, no. 3: 4780-4812.