we are struggling a little with the implementation of our MM2 force field for CDK.
There seems to be a problem with the bond stretch term in our implementation, which has a deep (possibly endless) minimum *deeper* and *apart* of the actual perfect bond-stretch value.
I'm not sure however, how the sum of all energy terms - the actually optimization objective - is behaving.
Of course, global optimization algorithms would always walk down into this deep valley instead of the actual requested bond length optimum.
I was wondering whether someone could comment on this? It this a bug (on our side) or a feature? Could it be the reason for the fact that many optimization algorithms (like steepest decent) are actually starting very close to the optimum?
So, to summarize: The question is whether the energy landscape defined by the MM2 forcefield equations might actually have minima *apart* and *deeper* than that of the desired correct geometry?
I would very much appreciate any hints.
Cheers,
Chris
-- Dr. rer. nat. habil. Christoph Steinbeck ([EMAIL PROTECTED]) Groupleader Junior Research Group for Applied Bioinformatics Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de) Z�lpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786
What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3..
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