ReviewMolecules (Basel, Switzerland)2019
Molecular Simulations with in-deMon2k QM/MM, a Tutorial-Review.
Review in Molecules (Basel, Switzerland), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Predicting Iron-Sulfur Cluster Redox Potentials: A Simple Model Derived from Protein Structures.ACS omega · 2025Article
- A Practical Guide to All-Atom and Coarse-Grained Molecular Dynamics Simulations Using Amber and Gromacs: A Case Study of Disulfide-Bond Impact on the Intrinsically Disordered Amyloid Beta.International journal of molecular sciences · 2024Article
- Simulating Electron Transfer Reactions in Solution: Radical-Polar Crossover.The journal of physical chemistry. B · 2023Article
- PdJournal of molecular modeling · 2023Article
- Aptamer-Based Point-of-Care Devices: Emerging Technologies and Integration of Computational Methods.Biosensors · 2023Review
- DFT exchange: sharing perspectives on the workhorse of quantum chemistry and materials science.Physical chemistry chemical physics : PCCP · 2022Review
- Combining Evolutionary Conservation and Quantum Topological Analyses To Determine Quantum Mechanics Subsystems for Biomolecular Quantum Mechanics/Molecular Mechanics Simulations.Journal of chemical theory and computation · 2021Article
- A simplified charge projection scheme for long-range electrostatics in ab initio QM/MM calculations.The Journal of chemical physics · 2021Article
- Analysis and visualization of energy densities. I. Insights from real-time time-dependent density functional theory simulations.Physical chemistry chemical physics : PCCP · 2020Article
Corrections and comments
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Authors and funding
14 authors.
Funding
Abstract
deMon2k is a readily available program specialized in Density Functional Theory (DFT) simulations within the framework of Auxiliary DFT. This article is intended as a tutorial-review of the capabilities of the program for molecular simulations involving ground and excited electronic states. The program implements an additive QM/MM (quantum mechanics/molecular mechanics) module relying either on non-polarizable or polarizable force fields. QM/MM methodologies available in deMon2k include ground-state geometry optimizations, ground-state Born-Oppenheimer molecular dynamics simulations, Ehrenfest non-adiabatic molecular dynamics simulations, and attosecond electron dynamics. In addition several electric and magnetic properties can be computed with QM/MM. We review the framework implemented in the program, including the most recently implemented options (link atoms, implicit continuum for remote environments, metadynamics, etc.), together with six applicative examples. The applications involve (i) a reactivity study of a cyclic organic molecule in water; (ii) the establishment of free-energy profiles for nucleophilic-substitution reactions by the umbrella sampling method; (iii) the construction of two-dimensional free energy maps by metadynamics simulations; (iv) the simulation of UV-visible absorption spectra of a solvated chromophore molecule; (v) the simulation of a free energy profile for an electron transfer reaction within Marcus theory; and (vi) the simulation of fragmentation of a peptide after collision with a high-energy proton.
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