It’s the combo of fix move with fix nve. You should not perform fix nve on the parts that move with fix move, as also explained in the docs of fix move.
I am wondering which command in my code is giving the warning message,
appreciate any help.
both fix move and fix nve will update atom positions, which in
'LAMMPS-speak' is called "time integrating".
fix 2 makes no sense at all, if you want to immobilize atoms, just don't
apply *any* time integration.
fix 3 and fix 4 should *only* be applied to the atoms that are not in the
groups upper or lower. otherwise your thermostat will be bogus and the
positions in the group upper are likely to be bogus.
for more details please see the documentation of the various fix styles
in question and also look up the explanation of the warning message in the
Errors section of the LAMMPS manual.