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A young man from the West visited Japan where he planned to be part a Zen monastery for a few months. Japanese Zen monasteries are very strict and disciplined about not moving during a sitting. Unaccustomed to sitting cross legged on the flow, the man had a lot of pain.
Finally, he felt the pain was too much so he gave up and told monastery authorities he was leaving. During his exit interview with the abbot, the young man asked: "If I were to say here another six months, would the pain go away?" The abbot replied, "No, but you wouldn't care anymore."
Meditation is an integral aspect of Buddhism and is essential for gaining wisdom. If, like the young man, you experience physical pain while meditating, don't rush to make yourself comfortable. Try sitting with the pain. Try analyzing it. Where specifically are you feeling it? Is it sharp or more like a throbbing pulse? What color could be assigned to the pain? This way, you actually make the pain your meditation focus. And, there's this bonus: you get to know it and you get to see if it eases and goes away. Of course, if the pain is sharp and unrelenting, you would be wise to make the necessary adjustment.