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The Blue Gene® project involves the development of a highly parallel supercomputer, the coding of scalable applications to run on it, and the design of protein simulations that take advantage of the power provided by the new machine. This paper provides an overview of analysis techniques applied to scientific results obtained with Blue Matter, the software framework for performing molecular dynamics simulations on the Blue Gene/L computer. Blue Matter is a portable environment that runs on several platforms ranging from single-processor to massively parallel machines. Since the Blue Gene/L computer has become available only recently, this work describes analysis techniques applied to a range of experiments of increasing complexity on a corresponding range of machine sizes, concluding with a membrane protein simulation currently running on a 512-node Blue Gene/L computer.
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