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? Thank you Steven -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
