Newton's  cradle are series of collision between two balls.
If the mass of all the balls are exactly the same, the energy will transfer from one side to another side (from one ball to the next one, ...). If the mass are not exactly the same , it is possible to cause all the ball moving (is this what you called vibration?)

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if put the newton's cradle in the water, what's happened?? and how it works in water?
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I would suggest you do the experiment and find out the ANSWER by yourself ;).