[gmx-users] Salt molecule - ion bond

[Justin A. Lemkul]

Chih-Ying Lin wrote:
> Hi
> The salt R-N(CH3)3-Br.
> 
> Could anyone tell me how to assign the force field parameter for the
> salt molecule ; especially for the ion bond/ ion angle/
> 

There will be no such thing, unless the force field has already assigned it. 
But since a covalent bond is probably unlikely to exist within such a compound 
(at least, in aqueous solution, for which most force fields are derived), you 
will likely not find a force constant (at the very least) for such a species.

> Does there exist "dihedral angle " between the ion Br and R ?
> And, any differences for assigning the Van-der waal and LJ parameters
> between salt and organic molecules?

If there's no bond, there's no dihedral either.  Again, I'm assuming aqueous 
solution.

L-J parameters are defined by the force field.  Investigate such issues in the 
the primary reference for the force field you want to use, and look in the 
*nb.itp for that force field, as well.

-Justin

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

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