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Keywords:

  • BlueGene;
  • PowerPC;
  • GROMACS;
  • SIMD optimization;
  • rounding;
  • table lookups

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. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011