Apple - How to slow down clock speed of processor

If your concern is how efficient your software is, let me suggest a more engineering-oriented solution that will let you keep your MacBook running at full speed:

Use the profiler built into Mathematica. This will let you identify the parts of your computations that consume the most time without having to resort to seat-of-the-pants measurements that only work on slow hardware.

I do not think it is possible to manipulate the minimum clock speed bar, simply because of the direct relation between power, frequency and the clock speed of a micro processor. Obviously the clock has a range, so for example for running simulations the system takes more power to run faster under the range, and then when you stop simulating you see the drop.

A Solution: Alternatively did you consider, running the programs within MAC OS but on an virtualizer (e.g., virtual box)? You can then limit the number of cores/RAM dedicating to running the second OS. In that case, the programs can forced to be run much slower; because the virtualizer has much lower resource. This will give you much more flexibility and in case of a failure, you can go back and change the virtualizer settings. More interestingly, you can bring the packaged settings that run on the virtualizer to another machine and run it there as well, by having the virtualizer there of course.