QM/MM Calculations with deMon2k

Salahub, Dennis R.; Noskov, Sergei Y.; Lev, Bogdan; Zhang, Rui; Ngo, Van; Goursot, Annick; Calaminici, Patrizia; Köster, Andreas M.; Alvarez-Ibarra, Aurélio; Mejı́a-Rodrı́guez, Daniel; Řezáč, Jan; Cailliez, Fabien; Lande, Aurélien de la

doi:10.3390/molecules20034780

Cited by 24 publications

(27 citation statements)

References 86 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Hamiltonian, for instance, the electric field created by sets of external charges as customarily done in hybrid QM/MM (Quantum Mechanical/Molecular Mechanical) approaches 28,29 . The total energy of such a composite system can be written as 30…”

Section: Kohn-sham Multicomponent Dftmentioning

confidence: 99%

Multicomponent density functional theory with density fitting

Mejı́a-Rodrı́guez

Lande

2019

The Journal of Chemical Physics

Self Cite

View full text Add to dashboard Cite

Multicomponent Density Functional Theory (MDFT) is a promising methodology to incorporate nuclear quantum effects, such as zero-point energy or tunneling, or to simulate other types of particles such as muons or positrons using particle densities as basic quantities. As for standard electronic DFT, a still ongoing challenge is to achieve the most efficient implementations. We introduce a multicomponent DFT implementation within the framework of auxiliary density functional theory, focusing on molecular systems comprised of electrons and quantum protons. We introduce a dual variational procedure to determine auxiliary electron and proton densities which leads to a succession of approximate energy expressions. Electronic and protonic fitted densities are employed i) in electronelectron, proton-proton and electron-proton classical Coulomb interactions, ii) in electron exchangecorrelation, proton-proton exchange, and electron-proton correlation potentials. If needed, exact exchange among electrons or among protons are computed by the variational fitting of the corresponding Fock potential. The implementation is carried out in deMon2k. We test various electron proton correlation functionals on proton affinities. We find that auxiliary densities can be safely used in electron-electron, proton-proton, and electron-proton classical Coulomb interactions as well as in electron-proton correlation, albeit with some precautions related to the choice of the electronic auxiliary basis set that must be flexible enough. Computational tests reported in the last section indicate that introduction of density fitting in MDFT is clearly advantageous in terms of computational effort with good scaling properties with respect to the number of electron and protons treated at the DFT level.

show abstract

Section: Kohn-sham Multicomponent Dftmentioning

confidence: 99%

Multicomponent density functional theory with density fitting

Mejı́a-Rodrı́guez

Lande

2019

The Journal of Chemical Physics

Self Cite

View full text Add to dashboard Cite

show abstract

“…We have used Cuby for QM/MM simulations of enzymatic reactions. The QM/MM methodology used in Cuby is described in detail in a separate paper . We have developed and used advanced simulation methods not available in conventional tools.…”

Section: Applicationsmentioning

confidence: 99%

“…In this case, the QM region covering the active site can be easily specified by the distance from the ligand and Cuby refines this selection so that a QM region compatible with the MM forcefield is constructed. Details on this functionality have been provided earlier . Various modifications of this scoring protocol have been successfully applied to multiple systems (see e.g.…”

Section: Applicationsmentioning

confidence: 99%

Cuby: An integrative framework for computational chemistry

Řezáč

2016

J Comput Chem

Self Cite

168

View full text Add to dashboard Cite

Cuby is a computational chemistry framework written in the Ruby programming language. It provides unified access to a wide range of computational methods by interfacing external software and it implements various protocols that operate on their results. Using structured input files, elementary calculations can be combined into complex workflows. For users, Cuby provides a unified and userfriendly way to automate their work, seamlessly integrating calculations carried out in different computational chemistry programs. For example, the QM/MM module allows combining methods across the interfaced programs and the builtin molecular dynamics engine makes it possible to run a simulation on the resulting potential. For programmers, it provides high-level, object-oriented environment that allows rapid development and testing of new methods and computational protocols. The Cuby framework is available for download at http://cuby4.molecular.cz. © 2016 Wiley Periodicals, Inc.

show abstract

“…This approach is used by AMBER (which has evolved from pure MM to contain some limited native QM functionality) and by GAUSSIAN and deMon2k (Salahub et al, 2015), both of which started as pure QM codes but now have some MM functionality. However, this approach seems, more often than not, to be of limited utility, as those who develop and maintain the software put most of their effort into the program's "strong suit."…”

Section: Introductionmentioning

confidence: 99%