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. ? ? - Deploying CHARMM in a Grid Computing Environment. ? ? - Development of the CHARMMing web site for facile CHARMM use.? ? - Development of a CHARMM tutorial web site.? ? With the Clovertown/quad core Intel systems we've now built 7 LoBoS clusters.? ? Two computer clusters with multi-core processors has been designed and procured which have 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. LoBoS VII was procured in FY07 and is undergoing acceptance testing. Performance results from this cluster so far appear promising. LoBoS VIII will have over 300 dual-quad core nodes connected by SDR and DDR InfiniBand by early calendar year 2009. Furthermore, the lab has procured large memory systems to expand its capability to perform very large calculations. Two machines with 64 GB of RAM are currently in service, and a requisition has been made for additional nodes with 128 GB of RAM. Finally, the amount of user storage available has more than doubled with the addition of new 24 bat storage servers to the computing environment. Integrating large memory machines with smaller memory machines allows for novel multi-scale applications involving large macromolecular systems. For example, vibrational subsystem analyis will be possible for very large multi-scale systems.? ? Work has continued to run CHARMM on computational grids. A large study on the effect of internal hydration on staphyloccocal nuclease has been completed on the Open Science Grid. Work is in progress to allow CHARMM to run in parallel (using MPI) in grid computing environments.? ? CHARMMing, a new graphical Web portal for CHARMM, has been developed. This project provides an easy to use front end to a small part of CHARMM's functionality. Users can perform energy calculations, minimization, solvation, normal mode analysis, and various types of dynamics (molecular dynamics, Langevin dynamics, and self-guided Langevin dynamics). QM/MM energy and minimization calculations are supported. A tutorial on the use of CHARMM is included. The portal has been integrated with PBS and Condor, making it suitable for use in cluster and grid computing environments. CHARMMing uses the Django web framework and most of its code is written in Python. The code is in the public domain and external users are welcome to download, run, and contribute to it. Development of the project is ongoing and plans are in place to add dynamic lessons along with several other features. This resource is to be found at www.charmming.org/ ? ? In collaboration with Dr. Stefan Boresch from the University of Vienna,? we are developing a new CHARMM tutorial that can be found at www.charmmtutorial.org/
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| Miller, Benjamin T; Singh, Rishi P; Klauda, Jeffery B et al. (2008) CHARMMing: a new, flexible web portal for CHARMM. J Chem Inf Model 48:1920-9 |
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| Woodcock 3rd, H Lee; Hodoscek, Milan; Gilbert, Andrew T B et al. (2007) Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations. J Comput Chem 28:1485-502 |
| Wu, Xiongwu; Brooks, Bernard R (2005) Isotropic periodic sum: a method for the calculation of long-range interactions. J Chem Phys 122:44107 |
| Petrella, Robert J; Andricioaei, Ioan; Brooks, Bernard R et al. (2003) An improved method for nonbonded list generation: rapid determination of near-neighbor pairs. J Comput Chem 24:222-31 |
| Wu, Xiongwu; Milne, Jacqueline L S; Borgnia, Mario J et al. (2003) A core-weighted fitting method for docking atomic structures into low-resolution maps: application to cryo-electron microscopy. J Struct Biol 141:63-76 |
| Wu, Xiongwu; Wang, Shaomeng; Brooks, Bernard R (2002) Direct observation of the folding and unfolding of a beta-hairpin in explicit water through computer simulation. J Am Chem Soc 124:5282-3 |
