Sorry for the time away-life...but here is a training I did recently on several exercises that fix one of the most common reasons for knee pain during squats(and lunges , running, or pain when going up and down stairs or getting up from a low chair). These have to do with how your hip controls your knee. Often when people try to treat knee pain by focusing on the quads like doing tons of knee extensions on a machine, wall sits, or hack squats, they often are taking care of a muscle that is already pretty strong. But, with the knee, it is often at the mercy of the joints above and below, the hips and ankles. Often knee pain isn't all about the quads at all. It is more about the muscles that control how your knee is positioned in relation to your foot. For example, when you squat, do your knees tend to come towards each other or do your feet rotate out. Often this is an issue with your hip abductors(i.e. your outer thigh muscles) and rotators not being able to control how your knee tracks. This often puts stress on the kneecap causing it to rub against the bone underneath causing pain.
When you fix how your knee and kneecap are tracking by reducing the amount of "knock-knee" posture your legs are in, you often take away the main irritation for the knees.
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