[gmx-users] rerun under non-bonded E. terms
jalemkul at vt.edu
Tue May 12 13:28:56 CEST 2015
On 5/12/15 6:58 AM, Albert Solernou wrote:
> 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 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
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