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