jalemkul at vt.edu
Mon Oct 20 02:48:28 CEST 2014
On 10/19/14 1:43 PM, Eric Smoll wrote:
> Hello Gromacs users,
> Here is a quote from a JPCB paper with over 500 citations:
> "In fact, in the specification of the OPLS-AA force field, sites within the
> same molecule separated by *more than* three bonds interact by
> Lennard-Jones and electrostatic potentials scaled by a factor of 0.5"
> Am I correct in assuming that "separated by more than three bonds" is a
> typo and should "separated by three bonds"? I have read the original OPLS
> reference (Jorgensen 1996) and it says:
> "it was found to be necessary to scale the 1,4-nonbonded interaction to
> permit use of the same parameters for inter- and intramolecular
> interactions. Scaling factors fij = 1/2 for both the coulombic and
> Lennard-Jones interactions emerged a the final choice..."
> There is no mention of this phrase in the additions and corrections
Probably a typo, but that's a question for the authors.
> Gromacs only scales the 1-4 interactions, not all nonbonded interactions
> beyond three bonds, correct?
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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