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Book Chapter

Scaling of the GROMACS 4.6 molecular dynamics code on SuperMUC.

MPS-Authors
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Kutzner,  C.
Department of Theoretical and Computational Biophysics, MPI for biophysical chemistry, Max Planck Society;

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Grubmüller,  H.
Department of Theoretical and Computational Biophysics, MPI for biophysical chemistry, Max Planck Society;

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2037317.pdf
(Publisher version), 177KB

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Citation

Kutzner, C., Apostolov, R., Hess, B., & Grubmüller, H. (2014). Scaling of the GROMACS 4.6 molecular dynamics code on SuperMUC. In M. Bader, A. Bode, & H. J. Bungartz (Eds.), Parallel Computing: Accelerating Computational Science and Engineering (CSE) (pp. 722-730). Amsterdam: IOS Press.


Cite as: http://hdl.handle.net/11858/00-001M-0000-0019-DB41-8
Abstract
Here we report on the performance of GROMACS 4.6 on the SuperMUC cluster at the Leibniz Rechenzentrum in Garching. We carried out benchmarks with three biomolecular systems consisting of eighty thousand to twelve million atoms in a strong scaling test each. The twelve million atom simulation system reached a performance of 49 nanoseconds per day on 32,768 cores.