Parallelization of AMBER molecular dynamics program for the AP1000 highly parallel computer

Abstract

The authors have parallelized the AMBER molecular dynamics program for the AP1000 highly parallel computer. To obtain a high degree of parallelism and an even load balance between processors for model problems of protein and water molecules, protein amino acid residues and water molecules are distributed to processors randomly. Global interprocessor communication required by this data mapping is efficiently done using the AP1000 broadcast network, to broadcast atom coordinate data for other processors' reference and its torus network; also for point-to-point communication to accumulate forces for atoms assigned to other processors. Experiments showed that a problem with 41095 atoms is processed 226 times faster with a 512 processor AP1000 than by a single processor.<>