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 2 . increases as O N , 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