A Family of Symplectic Integrators: Stability, Accuracy, and Molecular Dynamics Applications
SIAM Journal on Scientific Computing
Understanding Molecular Simulation: From Algorithms to Applications
Understanding Molecular Simulation: From Algorithms to Applications
Case study: an environment for understanding protein simulations using game graphics
Proceedings of the conference on Visualization '01
Blue Gene: a vision for protein science using a petaflop supercomputer
IBM Systems Journal - Deep computing for the life sciences
Early performance data on the blue matter molecular simulation framework
IBM Journal of Research and Development
Custom math functions for molecular dynamics
IBM Journal of Research and Development
Overview of the Blue Gene/L system architecture
IBM Journal of Research and Development
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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.