Title :
Grid-enabled applications in molecular dynamics simulations using a cluster of dedicated computers
Author :
Amisaki, Takashi ; Fujiwara, Shin-Ichi
Author_Institution :
Dept. of Biol. Regul., Tottori Univ., Japan
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.
Keywords :
grid computing; molecular dynamics method; parallel algorithms; parallel architectures; workstation clusters; Coulombic interactions; computation boards; dedicated cluster; dedicated computers cluster; grid-enabled applications; grid-enabled simulations; grid-enabling molecular dynamics calculation; molecular dynamics simulations; nonbonded pair interactions calculation; parallel fast multipole method; parallel platform; protein simulations; protein-water system; Application software; Biological system modeling; Biology computing; Computational modeling; Computer simulation; Grid computing; Hardware; Medical simulation; Power engineering computing; Proteins;
Conference_Titel :
Applications and the Internet Workshops, 2004. SAINT 2004 Workshops. 2004 International Symposium on
Print_ISBN :
0-7695-2050-2
DOI :
10.1109/SAINTW.2004.1268697
