In general you should be able to run your simulation iteratively by starting the simulation programatically using the MATLAB sim function (if you're not already familiar with the sim function, type doc sim on your command line to read the documentation)
So you would make a loop, something like this
simout = sim('myModel',...
Exactly how you assign the outputs to the inputs depends upon what kind of values you are changing. However if they are values of constant blocks or mask parameter values that are assigned to base workspace variables it is as simple as reassigning these base workspace values (as I indicated in the example above)