6533b7cffe1ef96bd1258f53
RESEARCH PRODUCT
New QM/MM implementation of the DFTB3 method in the gromacs package.
Gerrit GroenhofTomáš KubařKai Welkesubject
Theory methodComputer scienceMolecular simulationGeneral ChemistryExtended samplingFree energy simulationMolecular dynamicsDensity-functional tight-bindingComputational scienceQM/MMComputational MathematicsMolecular dynamicsQuantum TheoryThermodynamicsComputer Simulationta116Quantum mechanics/molecular mechanicsSoftwareProtein Bindingdescription
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.
| year | journal | country | edition | language |
|---|---|---|---|---|
| 2015-06-11 | Journal of computational chemistry |