HIGH PERFORMANCE SOFTWARE FOR BIOMOLECULAR DYNAMICS

该奖项解决了对耗时更少的模拟的需求 较大的生物分子系统，例如水膜系统 超过一万个原子。 最近推出的 三维快速多极子方法 提供了一个机会， 增强了分子动力学软件包。 非常合适的是 研究人员和他的合作者的一个计算机程序， MD，它与数据文件和处理例程接口， 一个流行的高分子建模软件包。 MD计划已经 用于测试计算方法，推进科学， 基准计算机系统。 PI将代码并入MD 实现了快速多极方法， 代码，并将联合收割机与距离类技术和简单的 高阶时间积分格式

This award addresses the need for less time-consuming simulations of larger biomolecular systems, for example water-membrane systems of more than ten thousand atoms. The recent availability of implementations of the three-dimensional fast multipole method presents an opportunity for the rapid implementation of enhancements to a molecular dynamics package. Highly suitable is a computer program of the investigator and his collaborators called MD, which interfaces to the data files and processing routines of a popular macromolecular modeling package. The program MD has been used to test computational methods, to advance science, and to benchmark computer systems. The PI will incorporate code into MD that implements the fast multipole method, will parallelize this code, and will combine it with distance class techniques and simple higher order time-integrated schemes.