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 (linear scaling methods). - 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 electron microscopy applications. - Implementation of IPS method for long range interaction calculation. - Development of 2D IPS method for membrane system simulation. - Improvement in Self-Guided Langevin Dynamics simulation algorithm. 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 V is a substantial improvement over previous systems in terms of both reliability and performance. In December, 2004, we completed this cluster with the addition of 62 new nodes, meaning that researchers now do not have to spend as much time waiting for computing resources to become available. This leads to faster simulation throughput and easier software development (due to quicker feedback on jobs). Starting with LoBoS IV, the clusters have used high-speed Myrinet interconnects and with LoBoS V we are increasingly using these to achieve higher performance with our existing software. Furthermore, over the past year we have upgraded the gigabit Ethernet infrastructure with a more reliable, wire speed managed switch. This has allowed for more efficient use of non-Myrinet cluster nodes to run parallel jobs and has reduced problems caused by network bottlenecks, the result of which is a better research computing environment. Clusters are also uniquely suited to very large applications since each compute node has its own disk (maximizing distributed I/O) and its workload may be configured to be independent of other nodes. As part of the development of the Replica/Path QM/MM method, we have created a novel way to parallelize these large scale quantum part of these calculations, making an ?embarrassingly parallel? and thus highly efficient algorithm. We have begun integrating this technique into CHARMM and testing it on LoBoS V.
| Borštnik, Urban; Miller, Benjamin T; Brooks, Bernard R et al. (2012) Implementation of the force decomposition machine for molecular dynamics simulations. J Mol Graph Model 38:243-7 |
| 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 |
| Woodcock, H Lee; Hodoscek, Milan; Brooks, Bernard R (2007) Exploring SCC-DFTB paths for mapping QM/MM reaction mechanisms. J Phys Chem A 111:5720-8 |
| 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 |
