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? 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. -- 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.