It's not how it was explained. Select nagasaki, go up to the rock, hold right stick down then rotate the left stick. You have to find the frequency. When the screen starts to rumble the most, hold it there for about 5 seconds. It doesn't require pressing up on the right stick.
The way I use it is, hold the right stick down, wiggle the left stick a bit, hold the right stick up, and then carefully rotate the left stick. When you find a position with the left stick that makes the whole screen shake, stop moving. Keep both sticks held exactly the way you have them. Eventually, the nagasaki will just do its thing, without any sort of "trigger" action like the other spells require.