No pair wise interaction within a molecule

Hello lammps users,

I have written a new pair class by modifying a pair_lj_cut_*. to implement a new lj like potential in lammps ( a Coarse grained model ). This works except for a one molecule system where the pairwise interaction among the beads ( intra-molecular ) is not calculated. I used a pair cutoff value of 2 (lj units) and the neighbor list settings are as default.

I know that pair/lj/cut 2.5 is calculating pair interaction among the beads within a molecule and this can be made off using neigh_modify exclude command.(i checked)

Is it the problem with the neighbor listing with lower force cut off or did i miss to modify some thing in the pair class ?

I find it difficult to understand the reason, could you please give some suggestion to sort out the problem ?

Check your output for any mention of special_bonds and make sure they are what you expect them to be. If not, issue a special_bonds comamnd to set it to what you want. In most models the non-bonded interactions between atoms neighboring in a molecule are disabled and I think this is also the default in LAMMPS.

Thank You !.
I found that, the non-bonded interaction are disabled among the atoms of a molecule. With special_bonds command it is possible to switch on non-bonded interaction in a molecule.

Thanks,

-----Sandeep.