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  1. Proceedings of the 3rd Workshop on General-Purpose Computation on Graphics Processing Units (GPGPU-3)
  2. Iterative induced dipoles computation for molecular mechanics on GPUs
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Toward exascale computational science with heterogeneous processing
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GPGPU role within a 500 TFLOPS heterogeneous cluster
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Implementing the PGI Accelerator model
Accelerating the local outlier factor algorithm on a GPU for intrusion detection systems
A mapping path for multi-GPGPU accelerated computers from a portable high level programming abstraction
Iterative induced dipoles computation for molecular mechanics on GPUs

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Iterative induced dipoles computation for molecular mechanics on GPUs

Content Provider ACM Digital Library
Author 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.
Starting Page 111
Ending Page 120
Page Count 10
File Format PDF
ISBN 9781605589350
DOI 10.1145/1735688.1735708
Language English
Publisher Association for Computing Machinery (ACM)
Publisher Date 2010-03-14
Publisher Place New York
Access Restriction Subscribed
Subject Keyword Molecular mechanics Induced dipoles Polarizable force fields Parallel programing Gpgpu
Content Type Text
Resource Type Article
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