Grid-enabled applications in molecular dynamics simulations using a cluster of dedicated computers

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.