MOLECULAR DYNAMICS SIMULATIONS OF BIOLOGICAL MACROMOLECULES

获得最佳性能所需的软件和硬件 仿真研究正在进行中。这些包括发展 用于大规模并行多指令/多数据的软件 (MIMD)机器，微编码商用处理器，以获得最佳 性能，以及工作站集群硬件和 作为一台并行计算机，相关软件可实现最佳性能。 大规模并行高性能计算机在以下方面大有可为 高速科学计算的未来。基于英特尔i860的 这种类型的机器正用于算法开发和 科学计算。对于具有128个处理器的系统，模拟 75倍的加速比(60%效率)是当前的水平 具有14,000个原子和13.5的大分子体系的性能 Angstrom非键相互作用截止距离。此类的方法 正在进一步设计和测试机器，目标是 将该系统用于未来的研究。 在以下方面，工作站群集提供了极具竞争力的环境 用于大分子模拟的性价比。一台工作站 基于惠普-730机的集群已经组装完成。 并行软件正在开发中，并被评为 网络连接功能(以太网、令牌环或光纤环 (FDDI)。正在为并行集群开发的软件 包括用于大分子模拟的CHARMM和LIGH、AND 美国国立卫生研究院开发的光线跟踪栅格图像分子图形程序。

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.