DATA MANAGEMENT ENVIRONMENT FOR MULTI SCALE BIOLOGICAL MODELING

该项目正在开发高效稳定的 并行机上的AMBER分子建模软件包， SDSC。 拟议的研究有两个一般方面： 分子动力学和最小化的细粒度实现 算法，然后是一个更粗粒度的免费并行化 能源计算。 去年的一个新方向是 粒子-网格埃瓦尔德码的并行化，沿着， 其他方面的改进。 一个涉及6万人的重大测试案例 原子系统正在进行中。 我们使用消息传递接口 (MPI)在阿贡实验室为我们的基本MD开发的编程模型 实施. 大多数供应商，包括英特尔、IBM和Cray/SGI， 支持MPI。 我们现在在集群上有（几乎）相同的并行代码 工作站和MPP机器上，如Cray T3 E，IBM的SP1和 SP2机器和凸示例SPP。 MPI实现是 现在是AMBER 5.0版本的标准部分，使其可用于 世界各地的工人。 代码开发一直是一个 合作努力，主要涉及约翰文森特和肯梅尔茨 (PSU)，汤姆Cheatham和彼得Kollman（加州大学旧金山分校），大卫案件（TSRI）， 杰里·格林伯格和杰克·罗杰斯（SDSC）。 Amber 5.1的发布 目前正在筹备之中，预计将于1998年秋季举行。 此版本将 由地方检察官协调 目前， 在最后的测试中包括：* 极大地改进了并行实现 粒子网格Ewald码; * 完全并行实现免费 能量扰动码 * 并行实现 “局部增强抽样”，动态的多拷贝方法 * 核磁共振结构精化约束的并行实现 明年的目标包括：（1）调整沟通 实现更接近理论预期性能的步骤 （2）额外的生产计算（DNA +盐+ 水），以测试和说明新代码的使用;（3）适应 用于自由能计算的粗粒度并行算法。

This project is developing efficient and stable implementations of the AMBER molecular modeling package on parallel machines for use at SDSC. There are two general aspects to the proposed research: a fine-grained implementation of the molecular dynamics and minimization algorithms, followed by a more coarse-grained parallelization of free energy calculations. A new direction in the past year is the parallelization of the particle-mesh Ewald code, along with further improvements in other areas. A major test case involving a 60,000 atom system is in progress. We use the Message Passing Interface (MPI) programming model developed at Argonne Labs for our basic MD implementation. Most vendors, including Intel, IBM, and Cray/SGI now support MPI. We now have (nearly) identical parallel code on clusters of workstations and on MPP machines like the Cray T3E, IBM's SP1 and SP2 machines, and the Convex Exemplar SPP. The MPI implementation is now a standard part of version 5.0 of AMBER, making it available to workers throughout the world. The code development has been a collaborative effort, involving primarily John Vincent and Ken Merz (PSU), Tom Cheatham and Peter Kollman (UCSF), David Case (TSRI), and Jerry Greenberg and Jack Rogers (SDSC). The release of Amber 5.1 is now being prepared and is expected in fall, 1998. This release will be coordinated by D.A. Case. Key parallel improvements that are now in final testing include: * Greatly improved parallel implementation of particle-mesh Ewald code; * Fully parallel implementation of free energy perturbation codes * Parallel implementation of "locally-enhanced sampling", a multiple-copies approach to dynamics * Parallel implementation of NMR restraints for structure refinement Goals for the coming year include: (1) tuning of the communication steps to achieve performance more like that expected on theoretical grounds; (2) additional production calculations (of DNA + salt + water) to test and illustrate the use of the new codes; (3) adapting coarse-grained parallel algorithms for free energy calculations.