High-Throughput Pairwise Point Interactions in Anton, a Specialized Machine for Molecular Dynamics Simulation

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Provided by: The University of Tulsa
Topic: Hardware
Format: PDF
Anton is a massively parallel special-purpose supercomputer designed to accelerate Molecular Dynamics (MD) simulations by several orders of magnitude, making possible for the first time the atomic-level simulation of many biologically important phenomena that take place over microsecond to millisecond time scales. The majority of the computation required for MD simulations involves the calculation of pair-wise interactions between particles and/or grid points separated by no more than some specified cutoff radius. In Anton, such range-limited interactions are handled by a High-Throughput Interaction Subsystem (HTIS).
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