Acquisition of a Computer System for Biophysical and Computational Chemistry

需要资金购买一台基于RISC架构的多处理器计算机，以取代Convex C220。所需设备将用于的项目包括：溶剂化蛋白质和液体的计算机模拟(R.M.Levy)、双螺旋DNA的计算机模拟(W.K.Olson)、生物分子结构和相互作用(H.M.Berman)、共轭分子中的内旋转势面(L.Goodman)、电子结构计算中的介质效应(K.Krogh-Jespersen)、核磁共振结构测定和蛋白质折叠(J.Baum)以及大分子复合体的结构和相互作用(M.Georgiadis)。需要基于RISC的多处理器是基于这些项目的计算密集型的性质，以及关于复杂生物分子系统的计算结果的可视化的需要。罗格斯大学以其在生物物理化学方面的研究计划的实力而闻名国际。将参与这项提议的研究人员联系在一起的一个中心主题是“生物分子结构和动力学”。生物大分子的复杂性和大小使得对这些系统的结构和动力学特征的分析需要大量的计算。这适用于理论研究，包括使用计算机图形学的分子建模、计算机模拟溶液中的生物分子以及生物分子和共轭分子的电子性质的量子化学计算。提案中提出的实验技术也是如此：大分子X射线结晶学和核磁共振光谱学。合作研究人员进行的单个项目都涉及到非常大规模的计算。分子生物物理学和计算化学的共享计算设施主要设在化学系内。生物物理化学计算资源的主干是Convex C220双处理器。1986年，在美国国立卫生研究院共享仪器基金的资助下，购买了一台Convex Cl单处理器。1989年，在国家科学基金会和罗格斯大学提供的仪器拨款的资助下，凸起被升级为双处理器C220。在购买时，Convex的矢量体系结构相当出色，提供的性能是它所取代的DEC VAX 780硬件的10-50倍。在当今的计算环境中，随着RISC计算机工作站的推出，Convex的性能就不那么令人印象深刻了。目前，Convex仅存的显著特征可能是其庞大的物理尺寸、动力要求和高昂的维护成本。我们建议用多处理器RISC计算机系统取代Convex C220。供应商的最终选择将在授予赠款后对替代RISC系统进行竞争性评估后做出。可能的供应商包括Silicon Graphics、Hewlett Packard、IBM和DEC。目前，我们正在认真考虑Silicon Graphics Power Onyx，主要是因为它具有高性价比的浮点性能，但也因为它的图形功能。我们的拟议预算是基于购买SGI Power Onyx系统，该系统配备8个R8000 90 Mhz处理器、2 GB高密度内存、现实引擎图形硬件和GB磁盘存储空间。

Funding is requested to purchase a multi-processor computer based on the RISC architecture to replace the Convex C220. The projects for which the requested equipment will be used include: Computer Simulations of Solvated Proteins and Liquids (R.M. Levy), Computer Simulations of Double Helical DNA (W.K. Olson), Biomolecular Structure and Interactions (H. M. Berman), Potential Surfaces for Internal Rotation in Conjugated Molecules (L. Goodman), Medium Effects in Electronic Structure Calculations (K. Krogh-Jespersen), NMR Structure Determination and Protein Folding (J. Baum), and Structure and Interactions of Macromolecular Complexes (M. Georgiadis). The need for the RISC based multi-processor is based on the computationally intensive nature of these projects, and the need for the visualization of the computed results concerning complex biomolecular systems. Rutgers University is internationally recognized for the strength of its research program in Biophysical Chemistry. A central theme connecting the investigators participating in this proposal is that of "Biomolecular Structure and Dynamics". The complexity and sheer size of biological macromolecules makes the analysis of the structural and dynamic features in these systems computationally intensive. This is true for the theoretical studies including molecular modeling using computer graphics, computer simulations of biomolecules in solution and quantum chemical calculations of electronic properties of biomolecules and conjugated molecules. This is also true of the experimental techniques that are represented in the proposal: macromolecular x-ray crystallography and NMR spectroscopy. The individual projects carried out by the coinvestigators all involve very large scale computations. The shared computational facilities for molecular biophysics and computational chemistry are housed primarily within the chemistry department. The backbone of the computational resources for biophysical chemistry is the Convex C220 dual processor. In 1986 a Convex Cl uniprocessor was purchased with funding from a National Institutes of Health Shared Instrumentation Grant. In 1989, with funding provided by an instrumentation grant from the National Science Foundation and by Rutgers University, the Convex was upgraded to a dual processor C220. At the time of its purchase, the vector architecture of the Convex was quite remarkable, providing 10-50 times the performance gains over the DEC VAX 780 hardware which it replaced. In the context of today's computing environment, with the availability of RISC computer workstations, the performance of the Convex is much less impressive. At present, perhaps the only remaining remarkable attributes of the Convex are its sheer physical size, its power requirements, and exhorbitant maintenance costs. We propose to replace the Convex C220 with a multi-processor RISC computer system. A final choice of vendor will be made after competitive evaluations of alternative RISC systems is carried out after the grant award. Possible vendors include Silicon Graphics, Hewlett Packard, IBM and DEC. At this time, we are seriously considering the Silicon Graphics Power Onyx primarily because of its cost effective floating point performance, but also because of its graphics features. Our proposed budget is based on the purchase of an SGI Power Onyx system with eight R8000 90 Mhz processors, 2 GByte high density memory, Reality Engine graphics hardware, and 64 GBytes of magnetic disk storage.