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Seminar by Dr. Tomas Kubar

Institute of Physical Chemistry and Center for Functional Nanomastructures, Karlsruhe (Germany)

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03 Jun 2015 11:00
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03 Jun 2015 12:00
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Lecture room 2009, Jülich GRS building (16.15)

The approximative density-functional method DFTB3 has been implemented in the
Gromacs package version 5, complementing the existing QM/MM interface. The tight
integration within the program gives rise to favorable eciency, and makes it possible
to employ a full PME-based treatment of QM/MM electrostatic interaction. Therefore,
unnecessary artifacts are avoided in simulations involving polar or even charged QM
regions. An appealing feature is that QM/MM calculations of potentials of mean force
are available, both with the Gromacs pull functionality and with the Plumed plugin.
Applications to several testing systems are presented. Free energy for the ultra-fast
proton transfer reaction in solvated malonaldehyde is obtained from umbrella sampling
as well as free simulations; the choice of reaction coordinate is discussed. The conforma-
tion of alanine dipeptide is investigated with both free simulations and metadynamics;
QM/MM and pure MM simulations are compared, as are various treatments of QM/MM
electrostatics. Finally, a cyclobutane thymine dimer lesion in DNA is simulated, both in
a neutral state and as a radical anion, which represents a metastable state.
Also discussed will be the issue of mobile molecules moving between QM and MM re-
gions. A new adaptive QM/MM scheme is introduced as a possible solution, avoiding any
discontinuities in the simulations and oering ecient parallelization of the calculation.


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