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持续价格降低和性能的提高，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。 当前项目包括： - Lobos，使用商品PC硬件的高性能计算机。 - 开发并行QM/mm方法，包括Q-chem的副本/路径 - 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的平行性能。 - 层析成像应用的EMAP方法的扩展。 - 图像对齐搜索和平均程序的开发。 - 开发用于膜系统模拟的2D IPS方法。 - 自引导的Langevin Dynamics（SGLD）仿真算法的改进。 - 为琥珀9的IP和SGLD算法开发。 - 开发一般独立的本地最大聚类程序。 - 提高CHARMM在网格计算环境中的效率。 - 新的多尺度工作，MSCALE，用于一般的多尺度建模。 - 双力场建模，CFF与Charmm力场 具有多核处理器的计算机群集已经设计和采购，这使科学家可以运行更大的模拟。 Lobos VI于2006年8月完成，添加了新的节点和基于Infiniband的新网络。该集群已经成功，为计算化学应用提供了更大的序列和并行性能。 下一个Lobos群集Lobos VII已在07财年购买，并在安装后将通过新的节点和新的双重数据速率（DDR）Infiniband产品来扩展这一成功，这些产品将使现有单元的网络带宽两倍。 在网格计算环境中部署charmm。对于许多生物学问题，单个模拟的运行提供了不足的数据。 为了启用和促进对大量模拟的运行和分析，我们已经在网格环境中部署了Charmm。工作是与威斯敏斯特大学的并行计算中心合作进行的，威斯敏斯特大学正在运行用于传统代码架构（GEMLCA）项目的网格执行管理以及开放的科学网格项目。自定义软件已开发为与开放的Scienge网格接口，并提供工作流程和工作管理。使用此方法运行了大规模生产的分子动力学模拟。 新的多尺度命令MSCALE已使用客户端服务器范式实施了CHARMMM程序。这允许一个人在Charmm框架内独立运行但连接的子系统。子系统可以是具有独立输入脚本的CHARMM工作，也可以是其他各种计算化学代码，例如从头算或分子力学程序。目前已经实施了以下AB INTIOM计划：NWCHEM，MOLPRO，GAUSSIAN，PSI和MPQC。 该实施还允许一个人在SUSBSYSTEMS和不同的系统尺度上混合不同的力场，例如粗粒，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，从而可以进一步提高AWSWISICY。 作为CHARMM的多尺度建模能力的一部分，该代码已被扩展为实现系统两个不同段的两个不同的力场。目标是正确解决合成聚合物表面上蛋白质吸附的固液多相系统。这样一来，CHARMM中的CFF实现已完全解耦，以便在Charmm中可以使用其他II类力场（例如PCFF和Compass）。 此外，现已实施CFF的图像粘结部件。在多乳酸（PLA）聚合物上，正在用实验肽吸附数据调整相间相互作用。 这项工作是与克莱姆森（Clemson）拉图尔（Latour）教授的持续合作。