Large biomolecular simulation on HPC Platforms I. Experiences with AMBER, Gromacs and NAMD

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DOI	10.5286/dltr.2009002
Persistent URL	http://purl.org/net/epubs/work/50963
Record Status	Checked
Record Id	50963
Title	Large biomolecular simulation on HPC Platforms I. Experiences with AMBER, Gromacs and NAMD
Contributors	HH Loeffler (STFC), MD Winn (STFC)
Abstract	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.
Organisation	CSE , STFC
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Language	English (EN)

Type	Details	URI(s)	Local file(s)	Year
Report	DL Technical Reports DL-TR-2009-002. STFC, 2009.		DLTR-2009-002.pdf	2009