RepRapFirmware on the Duet allows you to fine tune the behavior of the PWM controlled fans. Every fan is a little different, and to get the best performance and acoustics out of it, you may want to experiment with different PWM frequencies, etc.
More information on how fans are controlled with the M106 command here: Gcode dictionary
On the Ender 3 used in this guide the best (quietest) results were found by using a frequency of 20Hz.
Values lower than 20 would tend to pulse, and values higher than 60 had a high pitched whine. Values above 1000 would not spin up.
With these changes, you may not even be tempted to replace the stock fans with quieter options, saving you time and money.
Bear in mind that cooling performance may be slightly impacted by reducing the PWM frequency. If you notice excessive stringing or jamming, try increasing the frequency and see if it is solved.
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