Skip to main content
construction release_alert
Scholars@Duke will be undergoing maintenance April 11-15. Some features may be unavailable during this time.
cancel
Journal cover image

Accelerated molecular dynamics simulation with the parallel fast multipole algorithm

Publication ,  Journal Article
Board, JA; Causey, JW; Leathrum, JF; Windemuth, A; Schulten, K
Published in: Chemical Physics Letters
October 2, 1992

We have implemented the fast multipole algorithm (FMA) of Greengard and Rokhlin and incorporated it into the molecular dynamics program MD of Windemuth and Schulten, allowing rapid computation of the non-bonded forces acting in dynamical protein systems without truncation or other corruption of the Coulomb force. The resulting program speeds up simulations of protein systems with approximately 24000 atoms by up to an order of magnitude on a single workstation. Additionally, we have implemented a parallel version of the three-dimensional FMA code on a loosely coupled workstations, further reducing simulation times. Large (in both size of system and length of simulated time) protein molecular dynamics simulations are now possible on workstations rather than supercomputers, and very large protein computations are possible on clusters of workstations and parallel machines. © 1992.

Duke Scholars

Published In

Chemical Physics Letters

DOI

ISSN

0009-2614

Publication Date

October 2, 1992

Volume

198

Issue

1-2

Start / End Page

89 / 94

Related Subject Headings

  • Chemical Physics
  • 51 Physical sciences
  • 34 Chemical sciences
  • 10 Technology
  • 03 Chemical Sciences
  • 02 Physical Sciences
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Board, J. A., Causey, J. W., Leathrum, J. F., Windemuth, A., & Schulten, K. (1992). Accelerated molecular dynamics simulation with the parallel fast multipole algorithm. Chemical Physics Letters, 198(1–2), 89–94. https://doi.org/10.1016/0009-2614(92)90053-P
Board, J. A., J. W. Causey, J. F. Leathrum, A. Windemuth, and K. Schulten. “Accelerated molecular dynamics simulation with the parallel fast multipole algorithm.” Chemical Physics Letters 198, no. 1–2 (October 2, 1992): 89–94. https://doi.org/10.1016/0009-2614(92)90053-P.
Board JA, Causey JW, Leathrum JF, Windemuth A, Schulten K. Accelerated molecular dynamics simulation with the parallel fast multipole algorithm. Chemical Physics Letters. 1992 Oct 2;198(1–2):89–94.
Board, J. A., et al. “Accelerated molecular dynamics simulation with the parallel fast multipole algorithm.” Chemical Physics Letters, vol. 198, no. 1–2, Oct. 1992, pp. 89–94. Scopus, doi:10.1016/0009-2614(92)90053-P.
Board JA, Causey JW, Leathrum JF, Windemuth A, Schulten K. Accelerated molecular dynamics simulation with the parallel fast multipole algorithm. Chemical Physics Letters. 1992 Oct 2;198(1–2):89–94.
Journal cover image

Published In

Chemical Physics Letters

DOI

ISSN

0009-2614

Publication Date

October 2, 1992

Volume

198

Issue

1-2

Start / End Page

89 / 94

Related Subject Headings

  • Chemical Physics
  • 51 Physical sciences
  • 34 Chemical sciences
  • 10 Technology
  • 03 Chemical Sciences
  • 02 Physical Sciences