On Thu, Nov 22, 2007, Ilyas Yildirim wrote:
>
> The format of the frcmod file in
>
> http://amber.scripps.edu/formats.html#frcmod
>
> says that to define NONB terms for the new atom types, follow 10A, B or C.
> For dummy atoms, we want this NONB term to be zero. In my frcmod file, I
> have the following lines to define this NONB terms for the dummy atoms:
>
> -------------------------------
> NONB
> DH 1.0000 0.000
> -------------------------------
>
> I have tested this way of definition and it gives zero vdw energy for the
> dummy atoms.
>
> My question is the following: According to the format described in the
> above website, someone has to define NONB in the following ways:
>
> NONB SK
> (Slater-Kirkwood parameters are input)
>
> or
>
> NONB RE
> (van der Waals radius and the potential well depth)
>
> or
>
> NONB AC
> (The 6-12 potential coefficients)
>
> My question is, what is the right way to define this NONB terms? In DAC's
> TI tutorial, he also defines these NONB parameters without using SK/RE/AC.
> Thanks in advance.
I'm pretty sure frcmod only uses the "RE" form, and you don't have to specify
it. If in doubt, you can look at the code to make sure.
...dac
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Received on Sun Nov 25 2007 - 06:07:41 PST
