Error evaluation in the design of a special-purpose processor that calculates nonbonded forces in molecular dynamics simulations

✍ Scribed by Takashi Amisaki; Takaji Fujiwara; Akihiro Kusumi; Hiroo Miyagawa; Kunihiro Kitamura

• Publisher: John Wiley and Sons
• Year: 1995
• Tongue: English
• Weight: 897 KB
• Volume: 16
• Category: Article
• ISSN: 0192-8651
• DOI: 10.1002/jcc.540160906

✦ Synopsis

Special-purpose parallel machines that are plugged into a workstation to accelerate molecular dynamics (MD) simulations are attracting a considerable amount of interest. These machines comprise scalable homogeneous multiprocessors for calculating nonbonded forces (Coulombic and van der Waals forces), which consume more than 99% of the central processing unit (CPU) time in standard MD simulations. Each processor element in the machine has a pipeline architecture to calculate the total nonbonded force exerted on a particle by all of the other particles using information regarding the coordinates, the electric charge, and the species of each particle broadcast by the host computer. The processor then sends the calculated force back to the host computer. This article addresses the precision of the calculated nonbonded forces in the design of a processor LSI with minimal complexity. The precision of the arithmetic inside the processor that is required to calculate forces for MD simulations using Verlet's procedure was critically evaluated. Forward and