QM/MM Calculations with deMon2k

0444056 - ÚOCHB 2016 RIV CH eng J - Článek v odborném periodiku
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, Jan - Cailliez, F. - de la Lande, A.
QM/MM Calculations with deMon2k.
Molecules. Roč. 20, č. 3 (2015), s. 4780-4812. E-ISSN 1420-3049
Grant CEP: GA ČR GP13-01214P
Institucionální podpora: RVO:61388963
Klíčová slova: molecular dynamics simulations * polarizable force field * free energy path
Kód oboru RIV: CF - Fyzikální chemie a teoretická chemie
Impakt faktor: 2.465, rok: 2015
http://www.mdpi.com/1420-3049/20/3/4780/htm

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.
Trvalý link: http://hdl.handle.net/11104/0246724