Re: AMBER: fast 1/r methods

From: Andreas Svrcek-Seiler <svrci.tbi.univie.ac.at>
Date: Mon, 2 May 2005 16:18:22 +0200 (CEST)

Hi,
> I assume you guys are miles ahead of me on this. But on the off chance you
> haven't heard about this work in Karl Freed's group:

> A simple method for faster nonbonded force evaluations
> Min-Yi Shen, Karl F. Freed
> Journal of Computational Chemistry
> Volume 26, Issue 7 , Pages 691 - 698
>
....The same info can be obtained from entering "inverse squareroot" into
google or having a look into a standard numerics textbook (methods - 1st part) and
reading the intel compiler documentation or the amber(7 and up) sources
(methods - 2nd part). Speeding up CHARMM, AMBER, NAMD, GROMACS(!)... by
the shown factors would be pretty cool. Showing speedups for a package not designed
for speed (TINKER) seems close to cheating.

....I don't want to offend anyone by such a statement (sorry if I did) -
I just couldn't help writing this reply :-)

regards
Andreas

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Received on Mon May 02 2005 - 15:53:01 PDT