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When I'm doing a lot of running and then I ride the bike for a day, my knees hurt (more so the right one). Sometimes it is while riding, but usually it is after I ride and run next time. It goes away pretty quickly, but I'm wondering what it means. It's a pretty intense, non-specific ache throughout my whole knee. This also happens when I ride a lot then go to run. I think it's due to the different motions of bicycling and running, particularly with cycling as it doesn't feel natural to have my feet parallel as they are on the pedals. It feels like it is confining the natural motion (and flexing of the knee) to the circle the pedals trace. Oddly enough, it only affects running and biking, and doesn't make a peep of pain when walking, squatting, or doing weights.

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Mech, are you riding with click in pedals ? Perhaps the angle that your right foot sits on the pedal needs to be adjusted.
You could try riding with rat trap pedals for a while (no toe clips)
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That's what I have. I still think it's too narrow of an angle. To define it better, when on a bike the paths of the feet (viewed from above) are two parallel lines (since that's the only way the pedals move). When running, the paths of my feet are not parallel, and they intersect somewhere behind me. (Draw a diagram if you don't get the idea.) Or, if no one gets it, I'll draw one.
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I get what you are saying, and agree with what Phar is saying, I think maybe given that you run with your feet non-parallel maybe your clips need to be adjusted as such. or, you need pedals with a lot of float so you can kind of move to where it doesn't bother you. My mom and a good friend of mine both have issues with their knees and their bikes and it took a lot of tweaking and new pedals for my friend before they got it right. Another thing to think about is seat height, but since its one knee I think its your cleat/pedal.
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Also check that your seat isn't too low.

If your quad muscles tighten up, you will often feel pain in the knee. Make sure you do some quad stretches after riding and running, and you could also try some self massage of the quads.
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