Thank you for your reply.
please always reply to the mailing list, not just individual people. thanks.
So, my molecules are small (3-5 atoms). Can you point out an example of
building "molecule" neighbor list?
i don't think there is yet an *exact* match for what you are looking
for but something similar. but the airebo pair style compiles a list
of so-called "REBO neighbors" in the REBO_neigh() function, similarly
comb, bop and others have a list of "near" neighbors. what i am
suggesting is that you adapt this to rather then selecting by
distance, you would select by molecule id.
axel.