best thing for knees is massaging and heat, then light stretching once your knee has healed a bit. I've had buritis (burst fluid sacks in the knee) three times and that is what I did to reduce swelling and speed up the healing process. IBU Profen is also excellent to reduce inflamation. Every doctor I have spoken to has recommended it.
As for working out, if you are sore, take a hot bath and get/do a massage or the sore areas. this helps increase blood flow. Eating bananas and protein is also good because it helps the muscles recover. If I remember correctly, potassium is consumed in muscle cell contraction so bananas are a good way to replenish that. Also take some calcium as it is the main ion in muscle contraction and when it is all consumed, mucles charlie horse.
Do some light stretching of the sore muscles to prevent them from healing tighter than they were originally. Nothing extreme though, you don't want to pull them while they are weak.
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