Every once in a while I accidentally run myself into the ground over the weekend. I just switch to my geared bike for a few days and get back to normal pretty fast. If you are having more serious problems it may be from fit or gearing too high/low. Braking only with your legs will mess you up bad if you're not ready for it. It seems to use a different set of muscles than normal riding develops.
Take it slow for the first few months and you should be fine.