lammps to calculate thermal conductivity of molecular like water

Dear lammps-users
There is a problem has been bothering me for a long time.I want to use lammps to calculate thermal conductivity of molecular like water.
There are two methods (NEMD and EMD )calculating thermal conductivity.
if we use EMD like Green-Kubo, the thermal conductivity of water overestimates experiment values of water so much(30%-50%). However if we use NEMD like fix Heat or fix thermal/conductivity command(RNEMD), the energy of system is not conserved,the energy is increasing slowly.
So I really want to know if we can use lammps to calculate thermal conductivity of molecular,because lammps was designed for atomic systems not molecular ones.
Looking forward to your reply!
Jack zhuang