J.H.
I was told by my physical therapist when I complained of similar pain that I needed to do clams after running. Lay against the wall, back flat, knees bent and feet flat against the wall. You're going to open your legs, using the hip muscles to open. (http://www.mikereinold.com/2011/04/the-hip-external-rotat... )
I know you said it was your knee, on the inside, but that muscle goes from the groin/hip area all the way down and connects inside the knee. It can cause groin pain and knee pain. Try those and see if that helps at all.