DATA MANAGEMENT ENVIRONMENT FOR MULTI SCALE BIOLOGICAL MODELING

该项目正在开发高效和稳定的 在并行机上使用的琥珀分子建模程序包 SDSC.拟议的研究大致有两个方面：a 分子动力学和最小化的细粒度实现 算法，然后是更粗粒度的FREE并行化 能量计算。过去一年的一个新方向是 粒子网格Ewald代码的并行化，以及进一步的 其他方面的改进。一个涉及6万人的重大测试案件 原子系统正在进行中。我们使用消息传递接口 Argonne Labs为我们的基本MD开发的(MPI)编程模型 实施。现在，包括Intel、IBM和Cray/SGI在内的大多数供应商 支持MPI。我们现在在集群上拥有(几乎)相同的并行代码 工作站和MPP机器，如Cray T3E、IBM SP1和 SP2机器和凸模SPP。MPI的实现是 现在是琥珀5.0版的标准部分，使其可用于 世界各地的工人。代码开发一直是一个 协作努力，主要涉及约翰·文森特和肯·默茨 (PSU)，Tom Cheatham and Peter Kollman(加州大学旧金山分校)，David Case(TSRI)，以及 曾傑瑞·格林伯格和杰克·罗杰斯(SDSC)琥珀5.1的版本是 目前正在准备中，预计在1998年秋季。此版本将 由地方检察官案件协调。现在的关键并行改进 最终测试包括：*大大改进了并行实现 粒子网格Ewald代码；*FREE的完全并行实现 能量摄动代码*并行实现 “局部增强采样”--动力学的多副本方法* 用于结构细化的核磁共振约束的并行实现 来年的目标包括：(1)调整通信 实现更接近理论预期的绩效的步骤 地面；(2)额外的产量计算(DNA+盐+ 水)以测试和说明新规范的使用；(3)调整 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.