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

Abstract

Application of molecular dynamics (MD) simulations to large systems, such as biological macromolecules, is severely limited by the availability of computer resources. As the size of the system increases, the number of nonbonded forces (Coulombic and van der Waals interactions) to be evaluated increases as 𝒪(N2), 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 involving over 10,000 particles. Hence, the major target for reduction of the CPU time should be acceleration of the calculation of nonbonded forces. For this purpose, we developed a custom processor for calculating nonbonded interactions and a scalable plug-in machine (to a workstation), the MD Engine, in which numbers of the custom processors work in parallel. The processor has a pipeline architecture to calculate the total nonbonded force using the coordinates, electric charge, and species of each particle broadcast by the host computer. The force is calculated with sufficient accuracy for practical MD simulations. The processor also calculates virials simultaneously with forces for use in the calculation of pressure, accommodates periodic boundary conditions, and can be used in Ewald summations. An MD Engine system consisting of 76 processors calculates nonbonded interactions about 50 times faster than an UltraSPARC-I processor (Sun Ultra-2, 200 MHz) or an R10000 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 molecule immersed in a water sphere (13,258 particles) was accelerated by a factor of 48 using the MD Engine system. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 185–199, 1999