I think it really depends on what you use the structure for. If it's an initial guess to, say, and ab initio optimization then Geoff's proposal makes a lot of sense. If the structure and energy terms are to used as such, such as in Henry Rzepa's case, then you really need the "right" parameters. I think both are needed. Perhaps is Henry could supply the necessary parameters, or even snippets of code, for his systems of particular interest this would speed their implementation up? Meanwhile, better defaults in cases where parameters are totally missing might benefit many users? Jan >On Thu, 27 Jul 2006, Geoffrey Hutchison wrote: >>On Jul 27, 2006, at 2:36 AM, Tommi Hassinen wrote: >> >>>>Actually, what would be really nice is if the ghemical engine >>>>would substitute parameters from neighbors in the periodic table >>>>instead. So if I simulate Si and no parameters exist, it uses >>>>carbon but with a larger vdW radius. Same thing for Se using S >>>>parameters, etc. >>> >>>this would work pretty well for distances and radii, but I'm >>>afraid it would be too inaccurate for angle and torsion terms. :( >> >>You're telling me that it's more inaccurate than using hydrogen parameters? > >It's less inaccurate, you are right. But still I don't think it is a >useful approximation. The time and effort is better spent by adding >parameters for some specific elements instead (say Si for example). > >Regards, > > Tommi > >_______________________________________________ >ghemical-devel mailing list >ghemical-devel at bioinformatics.org >http://bioinformatics.org/mailman/listinfo/ghemical-devel -- =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Jan H. Jensen Associate Professor Department of Chemistry jhjensen at theory.ki.ku.dk University of Copenhagen Phone: +45 35 32 02 39 Universitetsparken 5 FAX: +45 35 32 02 14 2100 Copenhagen Denmark =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-