You can use several methods to obtain epsillon and mu so whatever simulation software you are using, you can obtain both transmission and reflection coefficients. Then you can use other equations relating refractive index (n) and impedance (z) with s11 and s21 to get the parameters with the help of MATLAB. This is the most common method. Check the link below for example, i will give you more materials on the same soon.
As Edgar and Hamza allude to above, there are many techniques to extract permittivity and permeability from S-parameters. I suggest the text below. It presents many such techniques and has a very good reference list. The book is a little dated but still very relevant.