Effective Floating Point Applications on FPGAs : Examples from Molecular Modeling ∗

While FPGAs have only one fifth the raw floating point capability of GPUs, other attributes allow them to be surprisingly competitive with respect to a number of critical floating point applications. In the first part of this extended abstract we review these FPGA attributes. In the second part we sketch three applications in molecular modeling where we have found FPGA performance to compare favorably: molecular dynamics, molecular docking, and discrete event molecular dynamics.

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