Nice thing you noticed. I ran 5 miles yesterday, while i never run, but i used to do long distance runs of about 20 miles 3 times a week when i was 15 years old. You never forget how to run
The thing i noticed is that if i concentrate on FEELING GOOD while running, all pain goes away and i can go on much longer / faster. Never focus on stopping the pain because it's a negative "mantra", but instead use something good as feeling light on your feet, feeling great and experience your breathing.