I've programmed the Arduino Uno to generate PWM corresponding to the serial input values. And it works fine with an LED. I took the connection from PWM pin 3 (where I set the output) to the base of a BC548 transistor and connected the motor in series with an external motor power supply (Vcc) and the collector and the emmitter is grounded (to both Arduino's GND pin and the external supply's). The motor had a fly wheel diode, 4N4007, and a capacitor of 1 µF for protection.
But when I connect the motor and provide it with the PWM input, it works for a few seconds and then I see a few flashes in the rx and tx LEDs, and it stops working even with a serial input or reset. I need to turn it off and then on to make it work again. The same thing repeats when I connect the motor, but it works fine with an LED.
How can I fix that??