Hi,
Suppose I have one polymer of beads 10 connected with springs. I specify this as one molecule. (all ten beads are in one molecule ). And I use pair_style lj. Will I have lj interactions with all other beads except connected ones( I mean 1-3, 1-4, 1-5…, 2-4, 2-5 ). do 3 ,4 ,5 come in 1’s neighbor list if I specify this as one molecule?
Hi Prathyusha,
If you want 1-3, 1-4, 1-5 etc.. LJ interactions to be considered, then use:
special_bonds 0.0 1.0 1.0
in your parm file.
the above command assumes that the LJ term for 1-3, 1-4 etc.. have
unit weight, i.e., they are treated at the same "level" as that
between beads of different polymer chains.
best,
bala
hi bala,
Hi Prathyusha,
If you want 1-3, 1-4, 1-5 etc.. LJ interactions to be considered, then use:special_bonds 0.0 1.0 1.0
small correction: with the current version of lammps this has to be
special_bonds lj/coul 0.0 1.0 1.0
cheers,
axel.