Development of molecular dynamics programs for proteins with a parallelized Barnes-Hut tree code

Author

Misoo, Kiyotaka ; Akiyama, Yutaka ; Shizawa, Yoshihisa ; Saito, Minoru

Author_Institution

Information & Math. Sci. Lab. Inc., Tokyo, Japan

Volume

2

fYear

2000

fDate

14-17 May 2000

Firstpage

1103

Abstract

We describe the design and the MPI-implementation of two parallel tree code molecular dynamics programs called MolTreC and Treecode AMBER, respectively. Both programs were developed using the parallel Barnes-Hut tree code for calculating Coulomb interactions which have been developed in earlier work. The parallel programs can rapidly calculate the Coulomb interactions of proteins in water without any cutoff approximations. They showed good speedups on distributed-memory multiprocessors and on PC clusters. MolTreC showed 111-fold speedup on SR2201 with 256 processors for the prowat benchmark of 11585 atoms. It was only 1.7-times slower than AMBER with 12A cutoff approximation.

Keywords

biology computing; distributed memory systems; molecular dynamics method; parallel algorithms; parallel programming; proteins; workstation clusters; Coulomb interactions; MPI-implementation; MolTreC; PC clusters; Treecode AMBER; distributed-memory multiprocessors; molecular dynamics programs; parallel programs; parallelized Barnes-Hut tree code; proteins; prowat benchmark;

fLanguage

English

Publisher

ieee

Conference_Titel

High Performance Computing in the Asia-Pacific Region, 2000. Proceedings. The Fourth International Conference/Exhibition on

Conference_Location

Beijing, China

Print_ISBN

0-7695-0589-2

Type

conf

DOI

10.1109/HPC.2000.843609

Filename

843609