Iterative induced dipoles computation for molecular mechanics on GPUs
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}
}
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.
November 5, 2010 by hgpu
