Assuming you defined the middle regions correctly
and the atoms in your groups are what you think they
are, then I don't know why you aren't getting heat transfer
between the end groups. Are you integrating the middle
with fix nve? Have you visualized the system? Is it
moving as you expect?
Can we calculate thermal conductivity using Green - kubo method in lammps??
If yes what is the function used to calculate it??
Not GK, except for the several posts on this topic recently,
where people have written their own fixes to do this. But LAMMPS
does it via another method in fix thermal/conductivity.