Hey Justin, I figured out how they calculated the sigma values. Basically they just take the geometric mean of nitrogen and oxygen sigma and epsilon from ffnonbed.itp file in OPLS-AA force field and calculated the pairwise LJ for N-O interaction.
Now I also try to add this information in my topol.top file. In order to do that as you have mentioned I added a section , [ nonbond_params ] ; i j func sigma epsilon opls_287 opls_272 1 0.323161248385416 0.790543521382599 after [ atoms ] section however I am facing with an error : Fatal error: Syntax error - File topol.top, line 42 Last line read: '[ nonbond_params ]' Invalid order for directive nonbond_params Any suggestion would be appreciated. > On 21 Jun 2017, at 16:46, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 6/21/17 10:39 AM, gozde ergin wrote: >> Hi MArk, >> Thanks for the respond. I understood that point however I still do not get >> which sigma to change. >> I the paper JCTC 2017, Miller et. al. they have mentioned that they increase >> the for nitrogen–carboxylate oxygen interactions in OPLSAA. >> However there are two sigma in oplsaa.ff/ffnonbonded.itp one for amino >> notrogen and one for carboxylate oxygen. >> >> sigma epsilon >> opls_287 N3 7 14.00670 -0.300 A 3.25000e-01 7.11280e-01 >> opls_272 O2 8 15.99940 -0.800 A 2.96000e-01 8.78640e-01 >> Which one defines the amino nitrogen–carboxylate oxygen interactions? >> Which sigma should I change? > > What people are doing more and more is introducing pair-specific parameters > to override the combination rule values. That's likely what is being > referred to. OPLS-AA by default does not use pair-specific LJ interactions, > hence why you find no [nonbond_params] in ffnonbonded.itp. The same is true > of AMBER. CHARMM uses some (also called NBFIX in the literature), while > GROMOS uses a ton of these. > > To override the LJ combination rules, add a [nonbond_params] directive with > the published parameters, which refer to an *interaction*, not an atom type. > > -Justin > >> Thanks >>> On 21 Jun 2017, at 16:21, Mark Abraham <mark.j.abra...@gmail.com> wrote: >>> >>> Hi, >>> >>> Different force fields work differently and thus are implemented >>> differently. Look at oplsaa.ff/ffnonbonded.itp and you will see that sigma >>> is a property of the atomtype >>> >>> Mark >>> >>> On Wed, Jun 21, 2017 at 4:16 PM gozde ergin <gozdeeer...@gmail.com> wrote: >>> >>>> Dear users, >>>> >>>> I am trying to change the sigma value of amino nitrogen–carboxylate oxygen >>>> interactions in OPLSAA in GROMACS. >>>> However I have difficulties to understand which parameter i should change >>>> in ffnonbonded.itp file? >>>> I am looking something like [ nonbond_params ] section however it is not >>>> exist in ffnonbonded.itp? >>>> Any help would be appreciated. >>>> >>>> Thanks in advance. >>>> -- >>>> 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. > > -- > ================================================== > > 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 <mailto:jalem...@outerbanks.umaryland.edu> > | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > <http://mackerell.umaryland.edu/~jalemkul> > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > <http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List> before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > <http://www.gromacs.org/Support/Mailing_Lists> > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users> or send > a mail to gmx-users-requ...@gromacs.org > <mailto: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.