QM/MM calculations with deMon2k

Dennis R. Salahub, Sergei Yu Noskov, Bogdan Lev, Rui Zhang, Van Ngo, Annick Goursot, Patrizia Calaminici, Andreas M. Köster, Aurelio Alvarez-Ibarra, Daniel Mejía-Rodríguez, Jan Řezáč, Fabien Cailliez, Aurélien De La Lande

Research output: Contribution to journalReview articlepeer-review

21 Scopus citations

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.

Original languageEnglish
Pages (from-to)4780-4812
Number of pages33
JournalMolecules
Volume20
Issue number3
DOIs
StatePublished - Mar 1 2015
Externally publishedYes

Keywords

  • Auxiliary DFT
  • Biomolecular modeling
  • Constrained DFT
  • Density functional theory
  • Double asymptotic expansion
  • QM/MM
  • Quantum Mechanical/Molecular Mechanical
  • deMon2k software

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