MOLECULAR DYNAMICS SIMULATIONS OF BIOLOGICAL MACROMOLECULES

点击翻译按钮获取中文摘要

Software and hardware required to obtain optimal performance for simulation research are being developed. These include the development of software for massively parallel Multiple Instruction/Multiple Data (MIMD) machines, microcoding commercial processors to obtain optimal performance, and the development of workstation cluster hardware and associated software for optimal performance as a parallel computer. Massively parallel high performance computers hold great promise for the future of high speed scientific computing. An Intel i860-based machine of this type is being used for algorithm development and scientific computing. For a system with 128 processors, simulation speedup of a factor of 75 (60% efficiency) is the current level of performance for a macromolecular system with 14,000 atoms and a 13.5 Angstrom nonbonded interaction cutoff distance. Methods for this class of machine are being further designed and tested, with the goal of using this system for future research. Workstation clusters provide a highly competitive environment in terms of cost performance for macromolecular simulations. A workstation cluster based on the Hewlett-Packard-730 machine has been assembled. Parallel software is being developed and is being evaluated as a function of network connectivity (Ethernet, Token ring, or fiber ring (FDDI). The software under development for the parallel cluster includes both CHARMM for macromolecular simulation, and LIGHT, an NIH-developed ray-trace raster image molecular graphics program.