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"The indiglos dim a little and so do the headlights a tiny bit when ever the bass hits hard. Is this an alternator problem or do I need to get one of those lightning bolt caps to store the voltage."
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Since your lights are only dimming when the bass hits hard(i.e. when the amp draws the most current), it sounds to me like you will need a capacitor(Lightning, Rockford Fosgate, Monster, etc.). Adding one certainly won't hurt anything.



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"Also can this dimming cause any damage?"
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As long as you don't add anything else to your system that would draw current, I don't *THINK* it can hurt anything. I'm not entirely sure, though, so don't quote me. I can say that if your lights are already dimming, if you add too much more to the current draw, it's possible to stall your car everytime the bass peaks.