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Hi, I am a new user to dynare and really appreciate your help with my problem.

There are several parameters, say A which I would like to estimate using Bayesian method in Dynare. I also have some other parameters in the model, say B which are some complicated function of A. Given values of A, I can only calculate B in Matlab (since Matlab has a function for this calculation). B doesn't influence the steady state of the model but only the dynamics of the model. I guess I can make an external Matlab file to calculate B and then use set_param_value in Dynare to call B when I do the Bayesian estimation? If so where should I put set_param_value? Under the parameters block? Or under the estimated_params block?

Thanks in advance for your help!

You cannot use the set_param_value command within the model. What you must do is either use model-local variables, which is hard in your case or use a steady state file. Within the steady state file, you can alter any parameter. An example is in the NK_baseline.mod.