Shifman M A, Windemuth A, Schulten K, Miller P L
Center for Medical Informatics, Yale University School of Medicine, New Have, CT 06510.
Proc Annu Symp Comput Appl Med Care. 1991:414-8.
Molecular dynamics simulations investigate local and global motion in molecules. Several parallel computing approaches have been taken to attack the most computationally expensive phase of molecular simulations, the evaluation of long range interactions. This paper develops a straightforward but effective algorithm for molecular dynamics simulations using the machine-independent parallel programming language, Linda. The algorithm was run both on a shared memory parallel computer and on a network of high performance Unix workstations. Performance benchmarks were performed on both systems using two proteins. This algorithm offers a portable cost-effective alternative for molecular dynamics simulations. In view of the increasing numbers of networked workstations, this approach could help make molecular dynamics simulations more easily accessible to the research community.
分子动力学模拟研究分子中的局部和整体运动。已经采用了几种并行计算方法来处理分子模拟中计算成本最高的阶段，即长程相互作用的评估。本文使用与机器无关的并行编程语言Linda开发了一种简单但有效的分子动力学模拟算法。该算法在共享内存并行计算机和高性能Unix工作站网络上都进行了运行。使用两种蛋白质在这两个系统上都进行了性能基准测试。该算法为分子动力学模拟提供了一种可移植的、具有成本效益的替代方案。鉴于联网工作站数量的不断增加，这种方法有助于使研究团体更容易进行分子动力学模拟。
