Development Of Advanced Computer Hardware And Software

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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. The primary efforts we have made include the development and refinement of parallel computing techniques suitable for macromolecular simulation and the construction of the hardware required to efficiently execute it. The latter task includes the evaluation of new hardware technology to ascertain the most cost effective methods of utilizing parallelized codes. Current projects include: - LoBoS, high performance computing machine using off the shelf 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 a new spatial-decomposition algorithm. - 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 stand-alone Local maximum clustering program. - Deploying CHARMM in a Grid Computing Environment. The LoBoS (Lots of Boxes on Shelves) system is an implementation of a "Beowulf" style high performance computing system using off the shelf hardware connected via high speed networks running the Red Hat Linux operating system. Since 1997, six Lobos computer cluster have been designed and constructed using commodity PCs. Historically, these systems have provided a greater than 10-fold improvement in price/performance when compared with systems from traditional supercomputing vendors. The early LoBoS systems demonstrated the effectiveness of this approach and were essential in the development of techniques to successfully manage these kinds of systems. LoBoS VI is an improvement over previous systems in terms of overall performance. In August, 2006, we completed this new cluster with the addition of new nodes and a new network based on Infinity Band. 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. The work is 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.