AMBER Archive (2008)

Subject: Re: AMBER: about glycam06

From: WANG,YING (wangying_at_ufl.edu)
Date: Sat May 03 2008 - 21:35:05 CDT

Thanks a lot!!

Ying

On Sat May 03 21:59:47 EDT 2008, "Austin B. Yongye"
<ayongye_at_chem.uga.edu> wrote:

> 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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> 

--
WANG,YING
Mechanical and Aerospace Engineering
University of Florida
Office: NEB 139
TEL: 001-352-846-3030

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