Re: AMBER: about glycam06

From: WANG,YING <wangying.ufl.edu>
Date: Sat, 3 May 2008 22:35:05 -0400 (EDT)

Thanks a lot!!

Ying


On Sat May 03 21:59:47 EDT 2008, "Austin B. Yongye"
<ayongye.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.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
>>>
>>> -----------------------------------------------------------------------
>>> The AMBER Mail Reflector
>>> To post, send mail to amber.scripps.edu
>>> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>>>
>>>
>>
>>
>>
>> --
>> WANG,YING
>> Mechanical and Aerospace Engineering
>> University of Florida
>> Office: NEB 139
>> TEL: 001-352-846-3030
>>
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber.scripps.edu
>> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
>



--
WANG,YING
Mechanical and Aerospace Engineering
University of Florida
Office: NEB 139
TEL: 001-352-846-3030
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun May 04 2008 - 06:08:03 PDT
Custom Search