Simulating reactions on Lammps

Use fix bond/break or use delete bonds command for deleting the bonds. For the atoms that are involved in bond deletion process change it to a different type after deletion. Overall the procedure involves defining multiple types prior to simulation and changing the atoms to a different type (but same LJ coeffs) once the bonds are deleted and make them not involve in bond formation (fix bond/create). Its not hard to implement. It can be done with existing lammps functionalities.