New QM/MM implementation of the DFTB3 method in the gromacs package

The approximate density‐functional tight‐binding theory method DFTB3 has been implemented in the quantum mechanics/molecular mechanics (QM/MM) framework of the Gromacs molecular simulation package. We show that the efficient smooth particle–mesh Ewald implementation of Gromacs extends to the calcula...

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Bibliographic Details
Published in:Journal of computational chemistry 2015-10, Vol.36 (26), p.1978-1989
Main Authors: Kubař, Tomáš, Welke, Kai, Groenhof, Gerrit
Format: Article
Language:English
Subjects:
Analytical chemistry
Binding sites
Biophysics
Computer Simulation
density-functional tight-binding
Deoxyribonucleic acid
DNA
extended sampling
free energy simulation
molecular dynamics
Protein Binding
quantum mechanics/molecular mechanics
Quantum physics
Quantum Theory
Simulation
Software
Thermodynamics
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Summary:The approximate density‐functional tight‐binding theory method DFTB3 has been implemented in the quantum mechanics/molecular mechanics (QM/MM) framework of the Gromacs molecular simulation package. We show that the efficient smooth particle–mesh Ewald implementation of Gromacs extends to the calculation of QM/MM electrostatic interactions. Further, we make use of the various free‐energy functionalities provided by Gromacs and the PLUMED plugin. We exploit the versatility and performance of the current framework in three typical applications of QM/MM methods to solve biophysical problems: (i) ultrafast proton transfer in malonaldehyde, (ii) conformation of the alanine dipeptide, and (iii) electron‐induced repair of a DNA lesion. Also discussed is the further development of the framework, regarding mostly the options for parallelization. © 2015 Wiley Periodicals, Inc. Hybrid QM/MM computational methods are a valuable tool to study biomolecular systems. Several appealing methods and programs were combined: Gromacs as an efficient molecular dynamics package; PLUMED as a free energy and extended sampling engine; and DFTB3 as a fast and reliable quantum chemical method. The resulting framework is versatile and efficient, as illustrated in several applications.
ISSN:0192-8651
1096-987X
DOI:10.1002/jcc.24029