Hi, The only thing that matters is that you understand how the force field constructs the interactions, and that your topologies do that :-)
Mark On Tue., 9 Jul. 2019, 22:09 Yunhui Ge, <tuf74...@temple.edu> wrote: > Hi, > > I have a question regarding Ryckaert-Bellemans dihedral potentials > (function type 3). In the manual of GROMACS 4.5.4 it says to use > Ryckaert-Bellemans type, one needs to erase the 1-4 interaction in [pairs] > section. My first question is what will happen if I use this potential > (type 3) but leave the 1-4 interaction in [pairs] section? > Next in the newer version GROMACS (5.1.4) the manual says: > > *In the original implementation of the potential for alkanes no 1-4 > interactions were used, which means that in order to implement that > particular force field you need to remove the 1-4 interactions from the [ > pairs ] section of your topology. In most modern force fields, like OPLS/AA > or Amber the rules are different, and the Ryckaert-Bellemans potential is > used as a cosine series in combination with 1-4 interactions.* > > What force field is considered as most modern force fields? (I'm using > AMBER ff99SB-ildn-nmr.) Again what will happen if I don't remove those 1-4 > interactions in the [pairs] section? > My last question is should I expect huge differences between > Ryckaert-Bllemans potential (type 3) and periodic (type 9) in simulations > of the same molecule? I plan to run some simulation to test that but I > wonder if there is a general answer based on the previous experience. Based > on the manual I know RB potential excludes 1-4 interactions whereas > periodic type include 1-4 interactions. I'm not clear about the performance > difference between these two dihedral types. Also if RB potential requires > the exclusion of 1-4 interactions why the manual says in modern force > fields it is used in combination with 1-4 interactions. > I'm familiar about this part and I do hope to learn more about this. Thank > you for your time in advance! > > Best, > > Yunhui > > 1. > -- > 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.