New QM/MM implementation of the DFTB3 method in the gromacs package
| Autor: | Gerrit Groenhof, Tomáš Kubař, Kai Welke |
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| Rok vydání: | 2015 |
| Předmět: |
Theory method
Computer science Molecular simulation General Chemistry Extended sampling Free energy simulation Molecular dynamics Density-functional tight-binding Computational science QM/MM Computational Mathematics Quantum Theory Thermodynamics Computer Simulation ta116 Quantum mechanics/molecular mechanics Software Protein Binding |
| Zdroj: | Journal of computational chemistry. 36(26) |
| ISSN: | 1096-987X |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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