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

Justin Lemkul jalemkul at vt.edu
Mon Jun 11 14:11:05 CEST 2018

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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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