Iterative induced dipoles computation for molecular mechanics on GPUs
2010 | conference paper. A publication with affiliation to the University of Göttingen.
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Iterative induced dipoles computation for molecular mechanics on GPUs
Pratas, F.; Mata, R. A. & Sousa, L. (2010)
Proceedings of the 3rd Workshop on General-Purpose Computation on Graphics Processing Units p. 111. 3rd Workshop on General-Purpose Computation on Graphics Processing, Pittsburgh Pennsylvania USA. DOI: https://doi.org/10.1145/1735688.1735708
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Details
- Authors
- Pratas, Frederico; Mata, Ricardo A. ; Sousa, Leonel
- Abstract
- 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.
- Issue Date
- 2010
- Conference
- 3rd Workshop on General-Purpose Computation on Graphics Processing
- ISBN
- 978-1-60558-935-0
- Conference Place
- Pittsburgh Pennsylvania USA
- Event start
- 2010-03
- Event end
- 2010-03
- Language
- English