Thank Justin. Mark you are right. I did not think about to check the manual.
Thanks again. > On 22 Jun 2017, at 15:51, Mark Abraham <mark.j.abra...@gmail.com> wrote: > > Hi, > > I'd start by looking in the documentation. Section 5.3.2 of the manual > clearly suggests putting it in the ffnonbonded.itp file, which is where you > expected to find it at the start of this thread, right? :-) > > Mark > > On Thu, Jun 22, 2017 at 3:47 PM gozde ergin <gozdeeer...@gmail.com > <mailto:gozdeeer...@gmail.com>> wrote: > >> 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> <mailto: >> jalem...@outerbanks.umaryland.edu >> <mailto:jalem...@outerbanks.umaryland.edu>> | (410) 706-7441 >>> http://mackerell.umaryland.edu/~jalemkul >>> <http://mackerell.umaryland.edu/~jalemkul> < >> 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> < >> 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? 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