Molecular Dynamics Calculations of Proteins on a "Hypercube"Machine

分子动力学技术的发展及其在蛋白质上的应用对计算时间提出了要求，而目前可用的资源显然无法满足这一要求。高度并行计算机提供了一个经济地满足这种需求的机会，但到目前为止，这种潜力尚未实现。这项工作将开发用于多肽和蛋白质分子动力学的软件修改，可选择在溶液中，特别是计算自由能差的选项。这一开发将在24节点并行计算机上进行，即新发布的“Chemputer”，这是一种具有超立方体架构的并行计算机。这台机器将与高效的分子动力学软件一起交付。计划是调整这个软件来执行最“现代”的计算。这些扩展将普遍可用。

The development of molecular dynamics techniques and their application to proteins has created demands for computing time that are demonstrably not being met by presently available resources. Highly parallel computers offer an opportunity to satisfy this need economically, but so far this potential has not been realized. This work will develop software modifications for doing molecular dynamics of peptides and proteins, optionally in solution, and specifically with options for computing free energy differences. This development shall take place on a 24-node parallel computer, the newly announced "Chemputer", a parallel machine with hypercube architecture. The machine will be delivered with efficient software for molecular dynamics. The plan is to adapt this software to perform the most "modern" calculations. These extensions will be made generally available.