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Large biomolecular simulation on HPC Platforms I. Experiences with AMBER, Gromacs and NAMD
HH Loeffler (STFC)
MD Winn (STFC)
We performed a general assessment of performance of the three molecular dynamics (MD) packages AMBER, Gromacs and NAMD on the four hardware platforms BlueGene/P, HP Cluster Platform 4000, HPCx and the UK?s current national flagship HECToR. The membrane-embedded Epidermal Growth Factor Receptor was chosen as a large system of biological interest. Results on a smaller soluble protein are provided to assess scaling with system size. We report the number of nano seconds per day and the relative speedup that can be achieved. The performance is discussed in detail and some general advice for MD simulation of large scale biological systems is given.
DL Technical Reports
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