The scanning tunnelling microscope (STM)-induced switching of a single cyclooctadiene molecule between two stable conformations chemisorbed on a Si(100) surface is investigated using an above threshold model including a neutral ground state and an ionic excited state potential. Switching was recently achieved experimentally with an STM operated at cryogenic temperatures (Nacci et al 2008 Phys. Rev. B 77 121405(R)) and rationalized by a below threshold model using just a single potential energy surface (Nacci et al 2009 Nano Lett. 9 2997). In the present paper, we show that experimental key findings on the inelastic electron tunnelling (IET) switching can also be rationalized using an above threshold density matrix model, which includes, in addition to the neutral ground state potential, an anionic or cationic excited potential. We use one and two-dimensional potential energy surfaces. Furthermore, the influence of two key parameters of the density matrix description, namely the electronic lifetime of the ionic resonance and the vibrational lifetimes, on the ground state potential are discussed.