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The need for strong conductive materials with which to build the rails and projectiles; the rails need to survive the violence of an accelerating projectile, and heating due to the large currents and friction involved. The force exerted on the rails consists of a recoil force - equal and opposite to the force propelling the projectile, but along the length of the rails (which is their strongest axis) - and a sideways force caused by the rails being pushed by the magnetic field, just as the projectile is. The rails need to survive this without bending, and must be very securely mounted.
I read another article which I can't seem to find now but it said something about only being able to fire the higher powered rail guns once before the rails got too bent out of shape to actually fire again without fixing them.
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