[gmx-users] Doubts in combination rules 2 and 3

[Justin Lemkul]

On 6/11/18 5:20 AM, Apramita Chand wrote:
> Please clarify these following doubts regarding combination rules in gromos
> force field:
>
> 1. The ffnonbonded.itp contains c6, c12 terms. If I choose combination rule
> 1 , it takes V and W as C6 and C12 as given. If combination 2 or 3 are
> chosen , then are the values converted to sigma and epsilon (Since for
> V=sigma and W=epsilon) and then used?

With combination rules 2 and 3, you have to *provide* sigma and epsilon, 
they're not converted.

> 2. If I have sigma and epsilon values for my molecule of interest, how do I
> add them to ffnonbonded.itp? Can I directly include sigma value under C6
> and epsilon value under C12 column?
> And then specify combination rule as 2 or 3?
>
> If so, how should I modify the non-bonded params section?
> Should I compute the interactions between atoms(according to the
> combination rule) and include them prior to simulation??

The [nonbond_params] directive is for pair-specific LJ interactions, 
i.e. those that do not obey normal combination rules. You do not need to 
do anything here unless your pair interaction(s) require special treatment.

-Justin

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

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