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Iterative induced dipoles computation for molecular mechanics on GPUs

Frederico Pratas,Ricardo A. Mata,Leonel Sousa
INESC-ID/IST, Rua Alves Redol, 9, 1000-029, Lisboa, Portugal
GPGPU ’10 Proceedings of the 3rd Workshop on General-Purpose Computation on Graphics Processing Units

@conference{pratas2010iterative,

   title={Iterative induced dipoles computation for molecular mechanics on GPUs},

   author={Pratas, F. and Mata, R.A. and Sousa, L.},

   booktitle={Proceedings of the 3rd Workshop on General-Purpose Computation on Graphics Processing Units},

   pages={111–120},

   year={2010},

   organization={ACM}

}

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In this work, we present a first step towards the efficient implementation of polarizable molecular mechanics force fields with GPU acceleration. The computational bottleneck of such applications is found in the treatment of electrostatics, where higher-order multipoles and a self-consistent treatment of polarization effects are needed. We have coded these sections, for the case of a non-periodic simulation, with the CUDA programming model. Results show a speedup factor of 21 for a single precision GPU implementation, when comparing to the serial CPU version. A discussion of the optimization and parameterization steps is included. Comparison between different graphic cards and a shared memory parallel CPU implementation is also given. The current work demonstrates the potential usefulness of GPU programming in accelerating this field of applications.
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