Development of Molecular Dynamics Programs for Proteins
with Parallelized Barnes-Hut Tree Code

Kiyotaka Misoo(1), Yoshihisa Shizawa(1),Yutaka Akiyama(2), Minoru Saito(3)

In this paper, we report on the design and the MPI-implementation of two parallel tree code MD programs called the MolTreC and the Treecode AMBER, respectively.
Both programs were developed using the parallel Barnes-Hut tree code 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 RWC PC clusters. (81-fold speedup on SR2201 with 256 PUs for the prowat benchmark of 11585 atoms.
It was only 1.7-times slower than the AMBER with 12 Angstrom cutoff approximation.)

(1) Information and Mathematical Science Laboratory, Inc. (2) Real World Computing Partnership (3) Hirosaki University