AMBER Archive (2008)

Subject: Re: AMBER: about glycam06

From: Austin B. Yongye (ayongye_at_chem.uga.edu)
Date: Sat May 03 2008 - 20:59:47 CDT

These two equations are essentially the same.
You can convert:
V(r) = 4*epsilon[(sigma/rij)^12-(sigma/rij)^6]
to
V(r) = (A/rij^12)-(B/rij^6)
by performing dV/dr = 0.
r = distance of minimum internuclear interaction
A = 4*(epsilon)*(sigma^12)
B = 4*(epsilon)*(sigma^6)

Ri in glycam would represent that internuclear distance for two identical
nuclei. Epsilon has its normal meaning.

For more information, you can check out page 206-ff of the book:
Molecular Modelling. Principles and Applications by Andrew R. Leach

Not sure if there are articles out there that simplify the explanations.
Austin-

> Thanks a lot!!
> I have one more question. The parameter of the lj potential of
> glycam06 are the A, B parameters of the 12-6 equation: like
> (A/rij^12)-(B/rij^6)
> Or the epsilon and sigma in this form:
> 4*epsilon[(sigma/rij)^12-(sigma/rij)^6]?
>
> Thanks!
>
> Best,
>
> Ying
>
>
>
>
> On Sat May 03 19:49:27 EDT 2008, "David A. Case"
> <case_at_scripps.edu> wrote:
>
>> On Sat, May 03, 2008, WANG,YING wrote:
>>
>>> Some of the specific dihedral interactions have various values,
>>> like
>>> CK-CG-CG-N
>>> , there are three values. Could anybody tell me the difference
>>> between them? Which one I should use?
>>
>> You (or rather programs) use all three: this single torsion has
>> three
>> components (of different periodicities) -- the actual potential
>> is the sum
>> of all three terms.
>>
>> ...dac
>>
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>
>
>
> --
> WANG,YING
> Mechanical and Aerospace Engineering
> University of Florida
> Office: NEB 139
> TEL: 001-352-846-3030
>
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