Journal
JOURNAL OF COMPUTATIONAL CHEMISTRY
Volume 36, Issue 26, Pages 1978-1989Publisher
WILEY
DOI: 10.1002/jcc.24029
Keywords
quantum mechanics; molecular mechanics; density-functional tight-binding; free energy simulation; extended sampling; molecular dynamics
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Funding
- Academy of Finland
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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. (c) 2015 Wiley Periodicals, Inc.
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