The most common cause of the pain you are describing is "Chondromalacia" (Refer illustration left). It most often appears in runners in their 20's and is associated with an increase in training and competition, including doing unfamiliar running drills, including over-striding, bounding up steps. Worst of all is running downhill. Another cause may be sore calf muscles which cause compensatory flat-footed striding with the backside dropping to the ground similar in appearance to running in a seated position (Bent knees has the patellae grinding hard on their femoral grooves).
Anything that causes excess grinding of the patellae on the underlying femoral groove will cause knee pain and a feeling of grating or grinding under the knee cap.
The cause of chondromalacia is usually never just one thing: It is usually a combination of several things all coming together to cause excess wear that exceeds the body's ability to repair. This includes lack of recovery time following hard races and following training. An occupation that involves a lot of bending at the knee, walking down stairs and even sitting for long periods with the knees bent may compromise repair of wear of the underside of the kneecaps.
Nutrition is important. If there are deficiencies or excesses of various nutrients, then repair may not be speedy and the repairs soft and weak. Glucosamine and chondroitin may assist and well worth taking for a period of three months at the daily recommended dosage. A Hair Tissue Mineral Analysis assists with determining any nutritional weaknesses may be contributing to wear exceeding repair.
If your knees are still bothering you, I think it is best to have a break of several days. Do some swimming and aqua-jogging. Get going with the glucosamine and chondroitin, ensure your diet is rich with protein and quality fats. While you are settling the knees down, try to identify everything that might have contributed to the knee pain and work out how to avoid these in the future. For example: Put in place the rule that you will have a relative rest day for every mile raced. So, if you raced 10 miles today, you do no running for the next two days then gradually resume to full training over the remaining 8 days. Got the idea?
Back to now: As your knees settle, resume running with care, just with jogging on a flat grassy surface. Run tall as if you are held up by a bungy cord attached to the top of your skull. If you have tight calf muscles, then get them massaged deeply and painfully on a weekly basis for as long as it takes for the deep massage to be pain-free. Get your quads, hamstrings and gluteals done while you are at it.
It is important to be patient and thorough when dealing with any kind of knee pain. Your knees have to last you many, many years. Please don't ruin them while so young.
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