Computation of induced dipoles in molecular mechanics simulations using graphics processors

J Chem Inf Model. 2012 May 25;52(5):1159-66. doi: 10.1021/ci200564x. Epub 2012 May 9.

Abstract

In this work, we present a tentative step toward 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 implemented a GPU accelerated code, based on the Tinker program suite, for the computation of induced dipoles. The largest test system used shows a speedup factor of over 20 for a single precision GPU implementation, when comparing to the serial CPU version. A discussion of the optimization and parametrization steps is included. Comparison between different graphic cards and CPU-GPU embedding is also given. The current work demonstrates the potential usefulness of GPU programming in accelerating this field of applications.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Molecular Dynamics Simulation*
  • Ubiquitin / chemistry
  • Water / chemistry

Substances

  • Ubiquitin
  • Water