Highlights of our Work
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We have installed a low-cost cluster of 32 PCs with 1.1GHz Athlon processors, 256MB of RAM, and switched fast ethernet. On this new platform, the freely available simulation code NAMD runs 1 ns of our 92K atom ApoA1 PME benchmark in 8 days with 70% efficiency, the equivalent of a 100 processor Cray T3E. The new machine will be useful for simulations such as the stretching of the muscle protein titin. This work seeks to examine in atomic detail the dynamics and structure-function relationships of this 30,000 amino acid long filament in muscle contraction and elasticity. The cluster also provides a powerful engine for interactive simulations. The Linux-based Scyld Beowulf operating system (see Scyld's press release regarding NAMD) makes the entire cluster appear to computational biologists as a single machine.