MOLECULAR DYNAMICS SIMULATIONS OF BIOLOGICAL MACROMOLECULES

生物大分子的分子动力学模拟

• 批准号: 3838545
• 负责人: B R BROOKS
• 金额: --
• 依托单位: CENTER FOR INFORMATION TECHNOLOGY
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/3838545
• 关键词: computer data analysis; computer program /software; computer simulation; computer system design /evaluation; computer system hardware; macromolecule; molecular dynamics

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.

获得最佳性能所需的软件和硬件 模拟研究正在进行中。 这些包括发展 大规模并行多指令/多数据软件 （MIMD）机器，微编码商业处理器以获得最佳 性能，以及工作站集群硬件和开发 相关软件可实现并行计算机的最佳性能。 大规模并行高性能计算机具有广阔的前景 高速科学计算的未来。 基于 Intel i860 的 这种类型的机器用于算法开发和 科学计算。 对于具有 128 个处理器的系统，仿真 目前的水平是 75 倍的加速（60% 效率） 具有 14,000 个原子和 13.5 的大分子系统的性能 埃非键相互作用截止距离。这个类的方法 机器正在进一步设计和测试，目标是 使用该系统进行未来的研究。 工作站集群在以下方面提供了高度竞争的环境 高分子模拟的性价比。 一个工作站 基于Hewlett-Packard-730机器的集群已经组装完毕。 并行软件正在开发中，并正在被评估为 网络连接功能（以太网、令牌环或光纤环） （FDDI）。 正在开发的并行集群软件 包括用于大分子模拟的 CHARMM 和 LIGHT（一种 NIH 开发的光线追踪光栅图像分子图形程序。