DEVELOPMENT OF A PARALLEL MOLECULAR-DYNAMICS CODE ON SIMD COMPUTERS -ALGORITHM FOR USE OF PAIR LIST CRITERION

In recent years several implementations of molecular dynamics (MD) cod es have been reported on multiple instruction multiple data (MIMD) mac hines. However, very few implementations of MD codes on single instruc tion multiple data (SIMD) machines have been reported. The difficulty in using pair lists of nonbonded interactions is the major problem wit h MD codes for SIMD machines, such that, generally, the full connectiv ity computation has been used. We present an algorithm, the global cut -off algorithm (GCA), which permits the use of pair lists on SIMD mach ines. GCA is based on a probabilistic approach and requires the cut-of f condition to be simultaneously verified on all nodes of the machine. The MD code used was taken from the GROMOS package; only the routines involved in the pair lists and in the computation of nonbonded intera ctions were rewritten for a parallel architecture. The remaining calcu lations were performed on the host computer. The algorithm has been te sted on Quadrics computers for configurations of 32, 128, and 512 proc essors and for systems of 4000, 8000, 15,000, and 30,000 particles. Qu adrics was developed by Istituto Nazionale di Fisica Nucleare (INFN) a nd marketed by Alenia Spazio. (C) 1998 John Wiley & Sons, Inc.