title: New QM/MM implementation of the DFTB3 method in the gromacs package.
abstract: 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.
authors.affiliation: Institute of Physical Chemistry and Center for Functional Nanostructures, Karlsruhe Institute of Technology, Karlsruhe, 76131, Germany.
authors.forename: Tomáš
authors.initials: T
authors.lastname: Kubař
authors.affiliation: Department of Chemistry, Nagoya University, Nagoya, 464-8602, Japan.
authors.forename: Kai
authors.initials: K
authors.lastname: Welke
authors.affiliation: Nanoscience Center and Department of Chemistry, University of Jyväskylä, Jyväskylä, 40014, Finland.
authors.forename: Gerrit
authors.initials: G
authors.lastname: Groenhof
mesh_terms: D003198:Computer Simulation; D011485:Protein Binding; D011789:Quantum Theory; D012984:Software; D013816:Thermodynamics
keywords: density-functional tight-binding; extended sampling; free energy simulation; molecular dynamics; quantum mechanics/molecular mechanics