[gmx-users] difference between force constants in various force field

[Justin Lemkul]

On 1/16/18 10:24 AM, kordzadeh at aut.ac.ir wrote:
> Hi every one
>
> I have a question
>
> I want to obtain topology of carbon nano tube with x2top but I must determine the value of bond strength and angle constant.
>
> I think we have a bond carbon-carbon that stretches with a constant force for example in amber force field this constant is 392459  kj /(mol nm^2) for interaction CA-CA but in gromos force field this constant is define differently....

There is no meaningful comparison that can be made between any 
parameters in different force fields. They all use different 
parametrization conventions, and in this case you're looking at AMBER 
(all-atom) vs. GROMOS (united-atom) and therefore aspects of the atoms 
themselves will be different (e.g. heavier masses on aliphatic C in GROMOS).

> I don't know what should I do
>
> I 'm confused, in gromos
>
> define gb_17   0.14    8.5400E+6
>
> C,CR1,CH2
>
>   
>
> 8.54 e 6 is force constant for stretch bond and dimention is kj/(mol nm^2), am I right?

No; GROMOS uses a quartic bond potential. See the manual and the 
discussion on this topic from yesterday.

> then we can conclude that if I want to determine force constant , I must select these constant wwith respect to force field ,
>
> I can't say these constants are same every where.rigth?
>
> is the dimention of constant kj/(mol nm^2) every where in gromacs, such as .itp files of force field, itp files that we receive form ATB and so on?
>
> any suggestion will be appreciated

If you need to develop new parameters or validate ones you have, you 
need to follow the methodology prescribed by the force field you're 
trying to use. For bonded force constants, this typically requires a QM 
vibrational frequency calculation and empirical fitting to reproduce the 
vibrational modes.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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