[ghemical-devel] Tripos 5.2

Jan H. Jensen jhjensen at theory.ki.ku.dk
Thu Jul 27 08:34:22 EDT 2006


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
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-


More information about the ghemical-devel mailing list