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

被引：2
|
作者：
Amisaki, T [1 ]
Fujiwara, S [1 ]
机构：
[1] Tottori Univ, Fac Med, Dept Biol Regulat, Yonago, Tottori 6838503, Japan
来源：
2004 INTERNATIONAL SYMPOSIUM ON APPLICATIONS AND THE INTERNET WORKSHOPS, PROCEEDINGS | 2004年
关键词：
D O I：
10.1109/SAINTW.2004.1268697
中图分类号：
TP [自动化技术、计算机技术];
学科分类号：
0812 ;
摘要：
A parallel platrorm 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.
引用
收藏
页码：616 / 622
页数：7
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