I’m going to post this back to the list so that other people may see your problem and be able to help you better than I can.
If I understand correctly, what you want to do is to perform a LAMMPS simulation coupled with a nudged elastic band method. If you are already writing the NEB method from scratch, why not made it as a module to LAMMPS like one of the other specialty fixes? If you are actually coupling a complete code with LAMMPS, have you tried using the instructions on coupling LAMMPS to other codes (http://lammps.sandia.gov/doc/Section_howto.html#4_10)..) Yes, that will probably require some programming on your part, but I think it will be far easier than coding up your own MD program.
On the other hand, someone else reading the expanded version of your problem may know an easier way to do what you want.
Best,
Joanne