Agreed, I've found jogging to be particularly good at clearing my mind. I like going to the gym in the afternoon for that reason: I can work for a while, and then take a break to jog when I inevitably get frustrated by something :)
If I may ask, what are you usually doing when you get those moments? I'd love to be able to spend time at the gym thinking, but usually when the blood flows out of my brain and down to my muscles, I'm lucky to be able to add two numbers together.
