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From the reference design of the Arduino UNO r3, I find that USBVCC will be connected to +5V via mosfet T1 if Vin is below 6.6V. Doesn't this short the two sources if Vin is just below 6.6V? The datasheet for regulator U1 (NCP1117) mentions input range as low as 6.5V for the 5V version.

This question came to mind when researching if I can simultaneously power the arduino with USB and the 5V-pin. There are many warnings not to do so, and some say its ok anyway. I realise that this will short the USB 5V with my external 5V if Vin/PWRIN is not connected or less than 6.6V/~7.3V, but how bad is that considering that this may happen anyway by design (if the theory above is correct)?

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If you connect a power supply directly to 5V pin on gpio it bypasses voltage regulator hence your board may be damaged if the power supply generates spikes. But you can power it using 5V supply directly to 5V pin provided you are using a good quality power supply. If you are supplying the power via Vin or power jack there is additional voltage regulator in path giving extra security. Thus you need more 6.5v so as the output of the regulator is 5v. If you supply 5v to Vin the output is nearly 4v thus the board doesn't get enough power.