[gmx-users] rerun under non-bonded E. terms

[Justin Lemkul]

On 5/12/15 6:58 AM, Albert Solernou wrote:
> Hi,
> I am getting fairly large values for the LJ energy term (order 10^8), while
> previous values were much better (order 10^5). I am wondering whether there is a
> radius decrease for bonded atoms or something equivalent to explain these
> differences. I browsed quickly the manual but could not find any clear explanation.
>
> Any ideas?

It comes from the fact that you're trying to treat everything as nonbonded when 
the functional forms were parametrized with exclusions of up to 3 bonds away. 
If two atoms are bonded, we don't parametrize their LJ interactions; they're 
excluded, so the functional form relies on parameters for "normal" nonbonded 
interactions.  Atoms that are bonded are usually well within the steep 
r^12-dominated part of the LJ curve.  I don't know what your goals are in doing 
this calculation, but they're likely not physically meaningful.

-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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