Hi Saeed, please mail questions like these to the LAMMPS user list. Neither I nor anyone else can fully answer the question you asked because you are the expert in the physical problem at hand. I suggest you check out the documentation and references for the two-temperature model (http://lammps.sandia.gov/doc/fix_ttm.html) and atomistic-to-continuum two-temperature model (http://lammps.sandia.gov/doc/fix_atc.html) fixes. That way you can determine if they have the methods necessary to accurately simulate the physics you care about.
Jeremy
You can use fix heat to heat a small region of the simulation box.
If you can ID the single molecule, you can put it in
a group, and use the velocity command to set its temperature
or velocities to whatever you want, then run a simulation.
Steve