Development of the MD-GRAPE,a High-Speed Accelerator with a Parallel Processor Design for Molecular Dynamics Simulations, and its Application to Studies of Biological Membranes

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Because of its great computational complexity, the use of molecular dynamics (MD) simulations for studying large systems like those of biological macromolecules is severely limited by the availability of computer resources. As the size of the system of interest increases, the number of non-bonded forces (Coulombic and van der Waals interactions) to be calculated increases as O(N2), where N is the number of particles in the system. Cutoffs of Coulombic interactions cause various detrimental effects and should be avoided. The calculation of non-bonded forces consumes more than 99% of the CPU time in and MD simulation involving over 10,000 particles. To overcome this problem, we have developed a special-purpose parallel machine that is plugged into a workstation to accelerate the calculation of non-bonded interactions. The machine is a scalable homogeneous multiprocessor called an "MD Engine". Each processor element in the machine, an LSI chip of about 130,000 gates fabricated with 0.8mm CMOS standard-cell technology, has a pipeline architecture to calculate the total non-bonded force using the coordinates, electric charge, and species of each particle broadcast by the host computer. After the force is calculated, the processor sends it back to the host. The MD Engine also calculates virials simultaneously with forces for use in the calculation of pressure, accommodates periodic boundary conditions, and can be used in Ewald summations. The precision of arithmetic operations inside the processor is optimized, and the force is calculated with sufficient accuracy for practical MD simulations. MD simulation of a Ras p21 protein molecule immersed in a water sphere (11,940 particles) was accelerated by a factor of 75 using an MD Engine system consisting of 24 processors and plugged into a SPARCstation 10/51.