VISUAL SIMULATION OF THE AMBER MOLECULAR DYNAMICS PROGRAM ON THE AP1000 HIGHLY PARALLEL COMPUTER

AMBER molecular dynamics program was parallelized for the AP1000 highly parallel distributed memory computer. Experiments showed that a problem with 41,095 atoms is processed 226 times faster with a 512 processor AP1000 than by a single processor. Visualization software was also developed for displaying three dimensional configurations of molecules computed by AMBER. Running this program concurrently with AMBER makes visual simulation of molecular dynamics possible.

[1]  Yasuhito Tanaka,et al.  Parallelization of AMBER molecular dynamics program for the AP1000 highly parallel computer , 1992, Proceedings Scalable High Performance Computing Conference SHPCC-92..

[2]  Hiroaki Ishihata,et al.  An architecture of highly parallel computer AP 1000 , 1991, [1991] IEEE Pacific Rim Conference on Communications, Computers and Signal Processing Conference Proceedings.

[3]  Hiroaki Ishihata,et al.  Low-latency message communication support for the AP1000 , 1992, ISCA '92.

[4]  Peter A. Kollman,et al.  AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions , 1981 .