[gmx-users] OPLSAA

[Dr. Vitaly Chaban]

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
>> 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
>> document.
>>
>
> 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?
>
>
> Yes.
>
> -Justin
>
> --
> ==================================================
>
> 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.
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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