Dr. Vitaly Chaban
vvchaban at gmail.com
Mon Oct 20 07:32:46 CEST 2014
Yes, it is a typo and not only in this paper.
There is NO plausible explanation why to introduce scaling factors for
the atoms separated by more than 3 bonds.
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Mon, Oct 20, 2014 at 4:48 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
>> 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
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> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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