Well, have you heard the acronym "RICE" for injury treatment? Rest, Ice, Compression, Elevation. Icing muscles reduces the swelling, and long runs create all these microtears in the muscles, essentially injuring them on a small scale (with the idea that they grow back stronger), so the immediate thing to do (within hours) is to ice them. But then you take a hot bath or soak in a hot tub in the evening or the next day, and that helps soothe the muscles.