Hello Cel,
what kind of behaviour are you expecting? It seems the model reaches a steady state after a relatively short time of about 100000ms and stays there until much later a periodic stimulus is applied (after 2.16e7 ms).
During the first ca 100000 ms I can see the behaviour changing if I change the initial concentrations, but these effects are long over when the first stimulus arrives. Essentially the system is in a steady state that is not much affected by the initial conditions.
There is one exception to this: The amoutn of 5htr4 (in bound and free form) is conserved in the model, so its initial value has some effect on the long term behaviour, I can see that the 5ht_out behaviour changes slightly with the initial value of 5HTR4.
Hope that helps,
Sven