Are you on about the trapezius muscle ?
If so simply rotating your head from side to side, rolling your head back and forwards under control, tilting your head from side to side a number of times will do the trick.
How many times ? Hey, everyone is different....!!!!!!!!! could take 20 - 30 head turns or even 50.........!
The nerve supply to the diaphragm is from the same root as the nerves that supply your shoulder area. When your diaphragm becomes 'tired' during exercise (just like any other muscle) you feel the discomfort in the shoulders because of that shared nerve supply. As Timpatient said, it's called referred pain.
Provided that you aren't doing anything funky with your shoulders when you run and just keep them relaxed, that is.