[gmx-users] united atom

[Justin Lemkul]

On 2/7/13 9:46 AM, Ali Alizadeh wrote:
> Dear All user
>
> There are 350 decane molecules in my simulation box,
>
> I like doing a simulation(npt ensemble) by a united atom force field,
> Can I use the opls (nonbonded: L-J 6-12 and coloumb) that is in
> gromacs?
>
> Beside, How can I neglect  coloumb interaction(non-bonded) and
> dihedrals(bonded)?
>

The OPLS force field in Gromacs contains both OPLS-AA (all-atom) and OPLS-UA 
(united-atom) types, so you could in theory use OPLS-UA, but that's a fairly 
ancient force field.  In that case, there are no Coulombic interactions anyway, 
because the united-atom carbons should not have any charge.  If you want to 
neglect dihedrals, I think you're hacking the force field in a way that makes no 
sense.

-Justin

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

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