Martin Horsch, Stefan Becker, Juan Manuel Castillo, Stephan Deublein, Agnes Fröscher, Steffen Reiser, Stephan Werth, Jadran Vrabec, Hans Hasse
Massively-parallel molecular dynamics simulation is applied to systems containing electrolytes, vapour-liquid interfaces, and biomolecules in contact with water-oil interfaces. Novel molecular models of alkali halide salts are presented and employed for the simulation of electrolytes in aqueous solution. The enzymatically catalysed hydroxylation of oleic acid is investigated by molecular dynamics simulation taking the internal degrees of freedom of the macromolecules into account. Thereby, Ewald summation methods are used to compute the long range electrostatic interactions. In systems with a phase boundary, the dispersive interaction, which is modelled by the Lennard-Jones potential here, has a more significant long range contribution than in homogeneous systems. This effect is accounted for by implementing the Janecek cutoff correction scheme. On this basis, the HPC infrastructure at the Steinbuch Centre for Computing was accessed and efficiently used, yielding new insights on the molecular systems under consideration.
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http://arxiv.org/abs/1305.4048
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