Hi Zoltan,
Yes, there is a way to change several options related to the ODE solver, including the absolute and relative tolerances. If your SimBiology model is in a variable m1, you can view all the options like this:
get(m1.getconfigset('active').SolverOptions)
You can then set the options like this:
m1.getconfigset('active').SolverOptions.AbsoluteTolerance = 1e-5;
Note that a new ODE solver option was introduced in R2012b, AbsoluteToleranceStepSize, which often (but not always) improves the quality of the solution by adaptively adjusting the absolute tolerance during the simulation. You may also try setting that option to false and see if that improves the quality of the results for your particular model.
Finally, I wanted to point out another feature that you might find useful in this situation. In R2012b, you can get a text view of the ODEs that SimBiology creates for your model using the new getequations method. For example:
equations = m1.getequations
Good luck with your modeling!
-Arthur
