Hello,
That does seem surprising. Here is what MIGHT be going on.
There is a feature (on by default) that automatically scales the absoluteTolerance on the ODE solvers in SimBiology.
That feature in combination with the fact that during fitting the following methods: fmincon, fminunc, lsqnonlin, lsqcurvefit, and scattersearch turn sensitivity analysis ON by default in order to compute gradients of the objective function, could be leading to having a different absolute tolerances between fitting and simulation.
If you indeed used one of the fitting methods mentioned above then you could test my hypothesis by turning off AbsoluteToleranceScaling. This can be done from the MATLAB command line (assuming m is the model):
>> cs = m.getconfigset;
>> cs.SolverOptions.AbsoluteToleranceScaling = false;
If you do this and refit the model (hopefully that is not too time consuming) then you can verify if the simulation gives you the same values.
Note that without AbsoluteToleranceScaling on you might have to adjust the absoluteTolerance by hand.
Let me know if this helps.
