Parallel molecular dynamics simulation of a protein

Abstract Program for energetic analysis of biochemical molecules (PEACH) is a software package for molecular dynamics (MD) simulation of biological molecules. The subroutines for the nonbonded interactions were modified to allow parallel computation by using the MPI library. The parallel efficiencies of the modified subroutines were close to 90% or better when using 32 processors of an IBM SP computer. The total performance was comparable to that of the special-purpose computer MD-GRAPE with 8 LSI chips.

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