Development Of Advanced Computer Hardware And Software

先进计算机硬件和软件的开发

• 批准号: 7594377
• 负责人: Bernard R Brooks
• 金额: $ 29.92万
• 依托单位: NATIONAL HEART, LUNG, AND BLOOD INSTITUTE
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/7594377
• 关键词: Address; Adsorption; Advanced Development; Algorithms; Amber; Architecture; Behavior; Biochemical Process; Biological; Biophysics; Boxing; Cereals; Chemistry; Class; Client; Code; Collaborations; Communities; Computational Biology; Computer Hardware; Computer Workstations; Computer software; Computers; Custom; Data; Data Analyses; Decompression Sickness; Development; Effectiveness; Environment; Evaluation; Facility Construction Funding Category; High Performance Computing; Image; Individual; Interphase; Laboratories; Ligand Binding; Linux; Liquid substance; Maintenance; Mechanics; Membrane; Methods; Modeling; Molecular; Motion; Network-based; Numbers; Object Attachment; Occupations; Operating System; Operative Surgical Procedures; Peptide Conformation; Peptides; Performance; Personal Computers; Pliability; Polymers; Price; Production; Property; Protein Subunits; Proteins; Range; Rate; Research Personnel; Resources; Running; Science; Scientist; Series; Simulate; Solid; Solvents; Speed; Structure; Structure-Activity Relationship; Supercomputing; Surface; System; Techniques; Technology; Time; United States National Institutes of Health; Universities; Vendor; Work; base; cluster computing; computational chemistry; cost effective; design; design and construction; enzyme substrate; human EML2 protein; improved; large scale simulation; molecular dynamics; molecular mechanics; multi-scale modeling; parallel computer; parallel computing; poly(lactic acid); programs; receptor; scientific computing; simulation; software development; success; tomography

With the continuing price reductions and performance increase in personal computer, workstation, and server hardware, computational chemistry researchers are able to develop and use more powerful software to study various theoretical problems and to conduct richer simulations of biochemical processes. Current projects include: - LoBoS, high performance computing machine using commodity PC hardware. - Development of parallel QM/MM methods including Replica/Path with Q-Chem - Development and support of the CHARMM computational chemistry software. - Increase the parallel performance of CHARMM via new spatial-decomposition and force-decomposition algorithms. - Expansion of the EMAP method for tomography applications. - Development of image alignment searching and averaging program. - Development of 2D IPS method for membrane system simulation. - Improvement in Self-Guided Langevin Dynamics (SGLD) simulation algorithm. - Development of IPS and SGLD algorithms for AMBER 9. - Development of a general stand-alone Local maximum clustering program. - Improving the efficiency of CHARMM in a Grid Computing Environment. - New multiscale effort, MSCALE, for general multiscale modeling. - Dual force field modeling, CFF with the CHARMM force field A computer cluster with multi-core processors has been designed and procured which has allowed scientists to run larger scale simulations. LoBoS VI, completed in August 2006, added new nodes and a new network based on InfiniBand. This cluster has been a success, delivering measurably greater serial and parallel performance for computational chemistry applications. The next LoBos cluster, LoBoS VII, has been procured in FY07 and, when installed, will expand on this success with with new nodes and new double data rate (DDR) InfiniBand products that will deliver twice the network bandwidth of the existing units. Deploying CHARMM in a Grid Computing Environment. For many biological problems, running of a single simulation provides insufficient data. To enable and facilitate running and analysis of a large number of simulations we have deployed CHARMM in a grid environment. Work has been performed in collaboration with the Centre for Parallel Computing from the University of Westminster who are running the Grid Execution Management for Legacy Code Architecture (GEMLCA) project and with the Open Science Grid project. Custom software has been developed to interface CHARMM with the Open Scienge Grid and to provide workflow and job management. A large scale production series of molecular dynamics simulations has been run with this method. A new multiscale command, MSCALE, has been implemented into CHARMMM program using a client-server paradigm. This allows one to run independent but connected subsystems within the CHARMM framework. The subsystems can be either CHARMM jobs with independent input scripts or a variety of other computational chemistry codes, such as ab initio or molecular mechanics programs. Currently the following ab initio programs have been implemented: NWCHEM, MolPro, Gaussian, Psi, and MPQC. The implementation also allows one to mix different force fields on susbsystems and also different system scales, such as coarse grain, atomic force fields, or QM at the same time. The controlling CHARMM script can run in parallel and the subsystems may also be independent parallel jobs, allowing for further aefficiency gains. As part of the multiscale modeling capability of CHARMM, the code has been extended to enable the use of two different force fields for two different segments of a system. The target was to properly address the solid-liquid multiphase system of protein adsorption on synthetic polymer surfaces. In doing so, the CFF implementation in CHARMM has been fully decoupled so that other class-II force fields such as PCFF, and COMPASS may be used in CHARMM. Additionally, the image bonding part for CFF has now been implemented. The interphase interaction is being tuned with experimental peptide adsorption data on Poly-lactic acid (PLA) polymers. This work is an ongoing collaboration with Prof. Latour at Clemson.

随着个人计算机、工作站和服务器硬件的价格不断降低和性能提高，计算化学研究人员能够开发和使用更强大的软件来研究各种理论问题并对生化过程进行更丰富的模拟。 目前的项目包括： - LoBoS，使用商用 PC 硬件的高性能计算机。 - 使用 Q-Chem 开发并行 QM/MM 方法，包括 Replica/Path - CHARMM 计算化学软件的开发和支持。 - 通过新的空间分解和力分解算法提高 CHARMM 的并行性能。 - 扩展 EMAP 方法的断层扫描应用。 - 开发图像对齐搜索和平均程序。 - 开发用于膜系统模拟的 2D IPS 方法。 - 自引导 Langevin Dynamics (SGLD) 模拟算法的改进。 - 为 AMBER 9 开发 IPS 和 SGLD 算法。 - 开发通用的独立局部最大聚类程序。 - 提高网格计算环境中 CHARMM 的效率。 - 新的多尺度工作，MSCALE，用于一般多尺度建模。 - 双力场建模，CFF 与 CHARMM 力场 已经设计并采购了具有多核处理器的计算机集群，使科学家能够运行更大规模的模拟。 LoBoS VI于2006年8月完成，添加了新节点和基于InfiniBand的新网络。该集群取得了成功，为计算化学应用提供了显着更高的串行和并行性能。 下一个 LoBos 集群 LoBoS VII 已于 2007 财年采购，安装后将通过新节点和新双数据速率 (DDR) InfiniBand 产品扩大这一成功，这些产品将提供两倍于现有设备的网络带宽。 在网格计算环境中部署 CHARMM。对于许多生物学问题，运行单个模拟提供的数据不足。 为了支持并促进大量模拟的运行和分析，我们在网格环境中部署了 CHARMM。这项工作是与威斯敏斯特大学并行计算中心合作进行的，该中心正在运行遗留代码架构的网格执行管理 (GEMLCA) 项目以及开放科学网格项目。定制软件已开发用于将 CHARMM 与 Open Scienge Grid 连接并提供工作流程和作业管理。已经用这种方法进行了大规模生产系列的分子动力学模拟。 新的多尺度命令 MSCALE 已使用客户端-服务器范例实施到 CHARMMM 程序中。这允许人们在 CHARMM 框架内运行独立但相互连接的子系统。子系统可以是具有独立输入脚本的 CHARMM 作业，也可以是各种其他计算化学代码，例如从头算或分子力学程序。目前已实施以下从头算程序：NWCHEM、MolPro、Gaussian、Psi 和 MPQC。 该实现还允许在子系统上混合不同的力场以及不同的系统尺度，例如同时粗粒、原子力场或 QM。控制 CHARMM 脚本可以并行运行，子系统也可以是独立的并行作业，从而进一步提高效率。 作为 CHARMM 多尺度建模功能的一部分，代码已得到扩展，可以为系统的两个不同部分使用两个不同的力场。目标是正确解决合成聚合物表面蛋白质吸附的固液多相系统。在此过程中，CHARMM 中的 CFF 实现已完全解耦，以便其他 II 类力场（例如 PCFF 和 COMPASS）可以在 CHARMM 中使用。 此外，CFF 的图像粘合部分现已实现。相间相互作用正在根据聚乳酸（PLA）聚合物上的肽吸附实验数据进行调整。 这项工作是与克莱姆森大学拉图尔教授持续合作的结果。