AMBER Archive (2006)

Subject: Re: AMBER: NONB values adjusted?

From: Dave S Walker (dswalker_at_uoregon.edu)
Date: Tue Nov 28 2006 - 13:48:36 CST

Thomas,

That cleared everything up. Thank you.

dsw

On Tue, 28 Nov 2006, Thomas Steinbrecher wrote:

> Dear Dave,
>
>> I'm trying to understand better the NONB values r* (and e). From following
>> the example on Van der Waals forces from the AMBER FAQs, it looks like the
>> r* value for TIP3P water is 1.738, as shown in the parmfiles. From reading
>> that example (as it pertained to Ca ion), to get the value of r*ij using
>> only water molecules would be (2)(1.738)=3.476. This is close to the 3.166
>> value commonly shown as the 'sigma' value in the literature, and I'm
>> wondering if there is some scaling factor that is missing, or are these
>> parameters supposed to be different? Thanks in advance.
>
> I think I ran across the same thing before, and here is what I think might
> account for the difference: There are two common formulations of the Lennard
> Jones Equation:
>
> E = 4u * [ 1/4 (r0/r)^12 - 1/2 (r0/r)^6 ] (1)
>
> and
>
> E = 4e * [ (s/r)^12 - (s/r)^6 ] (2)
>
> Here r0 and s (sigma) are two different parameters for the vdW distance, r0
> gives the minimum of the potential curve, s gives the point where E is zero.
> They are connected by r0 = 2^(1/6)*s. amber specifies its parameters
> according to (1) while most people normally think of (2) when they think of
> vdW potentials. So if you multiply the literature (sigma) value by ~1.122,
> you obtain an (amber style) r0 of 3.553. While this is not exactly what you
> report above, in my parm99.dat r0 for OW (water oxygen) is 1.7683. Also keep
> in mind that the designers of the amber force field might (?) have modified
> the vdW radius for oxygen to take into account the zero vdW radii on the
> water hydrogens.
>
> Kind Regards,
>
> Thomas
>
> Dr. Thomas Steinbrecher
> The Scripps Research Institute
> 10550 N. Torrey Pines Rd.
> San Diego CA 92037, USA
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