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Overview of molecular dynamics techniques and early scientific results from the Blue Gene project

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5 Author(s)
F. Suits ; IBM Research Division, Thomas J. Watson Research Center, P.O. Box 218, Yorktown Heights, New York 10598, USA ; M. C. Pitman ; J. W. Pitera ; W. C. Swope
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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.

Note: The Institute of Electrical and Electronics Engineers, Incorporated is distributing this Article with permission of the International Business Machines Corporation (IBM) who is the exclusive owner. The recipient of this Article may not assign, sublicense, lease, rent or otherwise transfer, reproduce, prepare derivative works, publicly display or perform, or distribute the Article.  

Published in:

IBM Journal of Research and Development  (Volume:49 ,  Issue: 2.3 )