You've got a test case that shows your tables do what you think they do, right? I would vary this setting and expect to see no effect.
Mark On Jun 12, 2013 10:03 AM, "Steven Neumann" <s.neuman...@gmail.com> wrote: > Whether it would be that easy i will find it. I specified my own potential > (not LJ) - so how come I should choose option 1 or 2 in nbfunct? I changed > h(x) in my table 6th column. > > > On Wed, Jun 12, 2013 at 1:18 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > On 6/11/13 4:12 PM, Steven Neumann wrote: > > > >> Dear Gromacs Users, > >> > >> I got really confused: In manual [defualts ]: > >> > >> "nbfunc is the non-bonded function type. Use 1 (Lennard-Jones) or 2 > >> (Buckingham)" > >> > >> I want to use mdrun -table table.xvg with my own potential, which one I > >> should choose? > >> > >> "gen-pairs - is for pair generation. The default is ‘no’, i.e. get 1-4 > >> parameters from the pairtypes list. When parameters are not present in > the > >> list, stop with a fatal error. Setting‘yes’ generates 1-4 parameters > that > >> are not present in the pair list from normal Lennard-Jones parameters > >> using > >> fudgeLJ" > >> > >> I want to have all intramolecular atoms (within my chain) interacting > (no > >> exclusions) with each other from [ atomtypes ] in ffnonbonded.itp > >> Does it mean "yes" with nrexcl =1 in my topology? > >> > >> And sth I also got confused: > >> > >> [ pairtypes ] are only 1-4 parameters or here I can specify parameters > for > >> all atoms within my molecule? So [ atomtypes ] in ffnonbonded.itp also > >> correspond to intra molecular interactions? > >> > >> > > These topics are discussed frequently. Please search the archive; surely > > you will find relevant topics. > > > > -Justin > > > > -- > > ==============================**========== > > > > Justin A. Lemkul, Ph.D. > > Research Scientist > > Department of Biochemistry > > Virginia Tech > > Blacksburg, VA > > jalemkul[at]vt.edu | (540) 231-9080 > > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin< > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > > > ==============================**========== > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/**mailman/listinfo/gmx-users< > http://lists.gromacs.org/mailman/listinfo/gmx-users> > > * Please search the archive at http://www.gromacs.org/** > > Support/Mailing_Lists/Search< > http://www.gromacs.org/Support/Mailing_Lists/Search>before posting! > > * Please don't post (un)subscribe requests to the list. Use the www > > interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists< > http://www.gromacs.org/Support/Mailing_Lists> > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists