[gmx-users] Mailing list issue fixed

David van der Spoel spoel at xray.bmc.uu.se
Fri Apr 30 10:59:01 CEST 2004

On Fri, 2004-04-30 at 10:39, Mu Yuguang (Dr) wrote:
> To what degree that you guys think, a well-developed, so-called,
> treecode algorithm for N-body problem can improve our MD simulation
> speeds ?
There is a paper by Petersen
  author = 	 {H. G. Petersen},
  title = 	 {Accuracy and efficiency of the particle mesh {E}wald
  journal = 	 BTjcp,
  year = 	 1995,
  volume =	 103,
  pages =	 {3668-3679}
where he compares these algorithms. IIRC the point where the tree code
(I assume you mean the fast multipole method) becomes more attractive is
at roughly 100,000 atoms. Now this number may or may not be very
accurate, but it is would be nice to try.

Meanwhile Erik and I are still working on optimizing the current code by
improving the parallellization.

David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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