I have estimated 'n4sid' model using System Identification Tool box and I saved this 'idss' type model into my currnet directory and loaded into Simulink file where i am analyzing the model. When i import this model into Simulink using a block called 'idmodel variable'and tested, results are not same as the results of 'compare' command in script file. I am sure, it is not because of initial conditions. Becuase i tried with the initial conditions which is given by 'compare' command. Also, if it is due to initial conditions, results must be same after it reaches steady state, but it is not same.
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