Grid-Enabled Applications in Molecular Dynamics Simulations Using a Cluster of Dedicated Computers

Authors:
Takashi Amisaki;Shin-Ichi Fujiwara
Affiliations:
-;-
Venue:
SAINT-W '04 Proceedings of the 2004 Symposium on Applications and the Internet-Workshops (SAINT 2004 Workshops)
Year:
2004

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Abstract

A parallel platform for molecular dynamics simulations and its grid-enabled use are reported. The platform is a cluster of PCs, each of which mounts dedicated computation boards that calculate nonbonded pair interactions. On this dedicated cluster, a parallel fast multipole method is used in cooperation with the special hardware to calculate Coulombic interactions, which is the most problematic part of protein simulations. Regarding a simulation of a protein-water system, the cluster (4 PCs with 2 boards each) was about 47 times faster than a PC without the special hardware support. In addition, we examined two approaches for grid-enabling molecular dynamics calculation using the dedicated cluster. This paper describes the designs and benchmark tests regarding these grid-enabled simulations as well as those on the dedicated cluster.