[gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

[Justin Lemkul]

On 6/21/17 10:55 AM, gozde ergin wrote:
> However in the paper they have mentioned that they increased the sigma  for amino nitrogen–carboxylate oxygen interactions
> by 0.13Angstrom   relative to the original value.
> So I assume there should be original value?
> However you mentioned that there is no pair-specific LJ interaction in OPLSAA.
> Even if I add a [nonbond_params] what epsilon and sigma should I use? Because they talk about the increment in sigma and I do not know the original value.
> Maybe I should connect them directly.
> 

Yes, do that to make sure they're consistent with the publication, but 
combination rules are explained in the PDF manual (and presumably in the 
original literature for the force field!) so you can calculate these very 
easily.  It's simple arithmetic.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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