I assume you mean PLECS Standalone when you said you only have PLECS? But anyway, we recommend the PLECS User Manual, available on our website at www.plexim.com/download/documentation, or the built-in Online Help as a resource for many questions on using the tool. In the Initialization Parameters window of the Simulation Parameters window in PLECS Standalone you can enter any valid MATLAB/Octave expression, consisting of MATLAB/Octave functions, operators, and variables. So this can directly be a code that is run to initialize variables, or you can reference by name an m file that sits in the same directory as the model. If you want to run multiple situations or start and modify a simulation or analysis, for example, there is both an internal scripting environment in PLECS Standalone, and a method for externally controlling PLECS Standalone. Both options are described in Chapter 10 "Simulation Scripts". Please let me know if you have further questions.