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 <jalem...@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. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.