title: Performance enhancements for GROMACS nonbonded interactions on BlueGene.
abstract: Several improvements to the previously optimized GROMACS BlueGene inner loops that evaluate nonbonded interactions in molecular dynamics simulations are presented. The new improvements yielded an 11% decrease in running time for both PME and other kinds of GROMACS simulations that use nonbonded table look-ups. Some other GROMACS simulations will show a small gain.
authors.affiliation: Computational Proteomics Group, John Curtin School of Medical Research, Australian National University, PO Box 334, Canberra, ACT, 2601, Australia. Mark.Abraham@anu.edu.au
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Abraham
mesh_terms: D056004:Molecular Dynamics Simulation; D012984:Software