Acceleration of molecular dynamics simulations using the fast multipole method and graphics processing units

Authors

  • D.F. Marin
  • V.L. Malyshev
  • E.F. Moiseeva
  • K.I. Mikhailenko
  • N.A. Gumerov
  • I.Sh. Akhatov

Keywords:

molecular dynamics
electrostatic interaction
fast multipole method
FMM
heterogeneous computations
GPU

Abstract

This work contains the speed-up results for the molecular dynamics simulations of electrostatic potentials in the application to water molecules. High-performance computations are achieved via the fast multipole method (FMM) for force calculation and the use of heterogeneous architectures, consisting of central and graphics processing units (CPU and GPU, respectively). FMM allows one to speed up the calculations of the far-field interactions by reducing the computational complexity from square complexity to the linear one. The use of the GPUs allows one to significantly speed up the computations. The realization of the FMM on GPU provides an opportunity to implement the computation experiments for large data sets. This paper shows that the method described has a great scalability and can be used to simulate the water dynamics for domains of 60 nm or for the number of molecules of over 10 million on personal workstations equipped with a single GPU.

New computational technologies

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Published

2013-11-06

Issue

Vol. 14 (2013): Issue 4.

Section

Section 1. Numerical methods and applications

Author Biographies

D.F. Marin

Bashkir State University
• Research Intern

V.L. Malyshev

Bashkir State University
• Research Intern

E.F. Moiseeva

Bashkir State University
• Research Intern

K.I. Mikhailenko

Bashkir State University
• Researcher

N.A. Gumerov

University of Maryland, Baltimore,
Институт передовых компьютерных исследований (UMIACS), 620 W. Lexington St., Baltimore, MD 2120, USA
• Professor

I.Sh. Akhatov

University of North Dakota
• Professor

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