Another way to do this is to make paremeters live in the MATLAB workspace as variables and just change them in between simulations. If you want the simulation to run for a set number of 'x' seconds, you can make StopTime a variable too. To get the resulting signals, yo can mark them for logging and retrieve them with the sim command like this:
param1 = 33;
param2 = 57;
stopTime = x;
[t1, signals1] = sim('yourModelName');
param1 = pi;
param2 = 0.5;
stopTime = x;
[t2, signals2] = sim('yourModelName');
By default, signals are columns in the second output, although that can be changed in the model settings.
Attacched is an example of this approach.
