I tend get some knee problems from too tight hamstrings (overworking the quads to fight against them).
+1 for climbing long, extended climbs on your bike. I did something close to a 10mi climb on Friday, and my hamstrings and calves got a major workout! I was extra sore because over some gravel patch before that climb my saddle moved back (and also pointed up, but I caught the angle issue but not the fore/aft issue before doing the climbing).




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