I had this problem. It stopped me from running for a few months. I was quite sad and went to see someone who specializes in running. He told me that the Oh SO Expensive running store that had assessed my gate did it incorrectly. Basically they had given me shoes for someone with over-pronation (or something similar) and I needed shoes for a neutral gate. They had also given me shoes that were too small - not so small that I could feel it, but they were slowly causing big, painful corns on my second to last toes that was also hindering running.
The right shoes corrected everything. Now I just have the minimal aches and pains of every jogger. I like to go everyday, on outside terrain, 5 miles, with one day a week off. Some days I purposely go slower, some faster - depending on how my muscles feel. I am very conscious of not pushing them to the limit... as then I would not be able to go the next day.
Ok, last word: shoes are SO important, you have no idea! Also, don't forget, if your feet are wider like mine, there is nothing wrong with trying out mens shoes.
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