When powering Arduino through Japan Jack at 12V USB communication becomes unstable and frequently interrupts/disconnects. Using Arduino Uno R3 and Linux on the connected computer.
Does anyone have any insight why this might be happening?
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12V is a little on the high end for what the arduino can handle by itself. If I were you I would use a DC step down Buck Converter module to hold the voltage at somewhere around 6v.
They're super cheap and pretty easy to use. Simply solder the + and - leads from your 12v power supply to the +in and -in on the buck converter. Then the + out and -out to the + and - for your arduino. Turn the potentiometer until you get somewhere around 6V.
Actually I was just reading online, and some people have trouble communicating with the arduino through USB while an external power source is connected. Internet says this problem is related to sharing voltages.