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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--
========================================
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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