[gmx-users] [ defaults ] and nonbonded

[Steven Neumann]

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