https://groups.google.com/forum/#!topic/jaamsim-users/-4eurpVqQeQ
If you know the different values you want to test in advance (static experiment), you can setup JaamSim to test these different values through the GUI interface. Also, you can setup a .cfg file to specify your baseline values, and then use separate files to identify just the differences in values you want to use in each treatment of your experiment.
On the other hand, if you don't know the next set of parameter values you want to try until you get the results from the current set of parameter values, then you're talking about a guided experiment. Perhaps you just want to explore the results space, spending more time in areas with lots of non-linearity for finer resolution; or perhaps you are optimizing.
The other part of your question is about the method of varying parameters. You can currently hand parameters to JaamSim from the command line. This allows you to program your loop in whatever language you want. It sounds like your preference would be to work from your IDE in Java though.