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We know that Amy and Rory had sex in the TARDIS while travelling through the time vortex on the night of their wedding, because that was when their daughter Melody Pond -- also known as River Song -- was conceived (explained in "A Good Man Goes to War"). We also know that they had sex on other occasions, though we don't have details of just when or how often, because they discovered that Amy was unable to have further children (revealed in "Asylum of the Daleks").