Ctrl+C works when the command window is the "current" or "chosen" window of MATLAB. You need to click on this window before doing ctrl+C.
You can save your data, by doing somehting like
save data.mat
in the middle of the loop where your simulation is running so that the data won't be lost. Your data ofcourse over-writes itself everytime you run
save data.mat
If your simulation is very long, you can do a smarted way of saving the data, by saving it every 5 min under different names for example, but watch not to flush your workspace memory.
