[gmx-users] converting the normal hormonic potential bond to Fourth power potential bond?

[Justin Lemkul]

On Wed, Apr 10, 2013 at 9:46 AM, 라지브간디 <rajiv at kaist.ac.kr> wrote:

> Dear gmx,
>
>
> I am getting confusion with converting the normal hormonic potential bond
> ( which is used in charmm27) to Fourth power potential bond ( gromos43a1).
>
>
> For Example.
> The value of C-O force constant, bond stretch and distance are in charmm
> is 518816.0, 0.123 and 0.12. Hence I used this value for converting to
> gromos type by using Fourth power potential bond equation and end up with
> value of 1.29189542054402. But the value of force constant in gromos for
> C-O is mentioned like this
>
>
> #define gb_4        0.1230  1.6600e+07
> ; C  - O        1200
>
>
> Here i dont understand what i am missing here.
>
>
> Some guidance or suggestion or really appreciated. Thanks.
>
>
Equation 4.38 from the 4.6.1 manual yields a force constant of
approximately 17146407, which is right in the ballpark of the actual
Gromos96 value. You're not going to get exact agreement between force
fields since they use different parameters.

-Justin

-- 

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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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