Abstract
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 Janeček 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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Acknowledgements
The present work was carried out under the auspices of the Boltzmann-Zuse Society for Computational Molecular Engineering (BZS), and the molecular simulations were conducted on the XC4000 supercomputer at the Steinbuch Centre for Computing, Karlsruhe. The authors would like to thank Akshay Bedhotiya (Bombay) for his assistance regarding the simulation of gas bubbles and Sergey Lishchuk (Leicester), Martin Buchholz, Wolfgang Eckhardt, and Ekaterina Elts (München) and Gábor Rutkai (Paderborn) as well as Martin Bernreuther, Colin Glass, and Christoph Niethammer (Stuttgart) for contributing to the development of the ls1 mardyn and ms2 molecular simulation programs as well as Deutsche Forschungsgemeinschaft (DFG) for funding the Collaborative Research Centre (SFB) 926. Furthermore, they would like to acknowledge fruitful discussions with Cemal Engin, Michael Kopnarski, Birgit and Rolf Merz as well as Michael Schappals and Rajat Srivastava (Kaiserslautern), George Jackson and Erich Müller (London), Jonathan Walter (Ludwigshafen), Philippe Ungerer and Marianna Yiannourakou (Paris) as well as Nichola McCann (Visp).
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Horsch, M. et al. (2013). Molecular Modelling and Simulation of Electrolyte Solutions, Biomolecules, and Wetting of Component Surfaces. In: Nagel, W., Kröner, D., Resch, M. (eds) High Performance Computing in Science and Engineering ‘13. Springer, Cham. https://doi.org/10.1007/978-3-319-02165-2_45
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DOI: https://doi.org/10.1007/978-3-319-02165-2_45
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