Development of MD engine: High-speed accelerator with parallel processor design for molecular dynamics simulations

Application of molecular dynamics (MD) simulations to large systems, such a s biological macromolecules, is severely limited by the availability of com puter resources. As the size of the system increases, the number of nonbond ed forces (Coulombic and van der Waals interactions) to be evaluated increa ses as O(N-2), where N is the number of particles in the system. The force evaluation consumes more than 99% of the CPU time in an MD simulation invol ving over 10,000 particles. Hence, the major target for reduction of the CP U time should be acceleration of the calculation of nonbonded forces. For t his purpose, we developed a custom processor for calculating nonbonded inte ractions and a scalable plug-in machine (to a workstation), the MD Engine, in which numbers of the custom processors work in parallel. The processor h as a pipeline architecture to calculate the total nonbonded force using the coordinates, electric charge, and species of each particle broadcast by th e host computer. The force is calculated with sufficient accuracy for pract ical MD simulations. The processor also calculates virials simultaneously w ith forces for use in the calculation of pressure, accommodates periodic bo undary conditions, and can be used in Ewald summations. An MD Engine system consisting of 76 processors calculates nonbonded interactions about 50 tim es faster than an UltraSPARC-I processor (Sun Ultra-2, 200 MHz) or an R1000 0 processor (SGI Origin 200, 180 MHz). On a Sun Ultra-2 workstation with a single UltraSPARC-I processor an MD simulation of a Ras p21 protein molecul e immersed in a water sphere (13,258 particles) was accelerated by a factor of 48 using the MD Engine system. (C) 1999 John Wiley & Sons, Inc.