Let me preface my answer with a disclaimer: All of my experience PWM'ing motors is with speed control of cooling fans. Your application will certainly differ, at least a little bit.
The way I find the minimum duty cycle, I look for the minimum that will allow the motor to start spinning. With standard muffin fans, this is about 40%. Then I add a small margin just to be safe. I find this by applying 0% duty cycle and slowly ramping it up until the motor starts spinning.
This startup power is higher than the amount of power required to keep the motor spinning once it has already spun up. With fans, this is somewhere in the 20-30% range. In other words, if I wanted to spin a fan really slow, I would have to apply 40% to get it moving and then I could back down to 20-30%.
Normally, just to be safe, I do not go below the startup power. That way I can be sure that the motor is spinning, although it does limit the minimum speed that I can do.
There are problems with this, however. Many things can affect the startup power requirements. Temperature, motor loading, age, dust, different motor lots, etc. You have to take all this into account, and built in some power margin.
Alternatively, you have to monitor your motor through a tachometer or something similar. Then have some motor control software do the appropriate thing if the motor is spinning too fast or too slow. Good motor control software will automatically take into account the startup power and other things.
If you don't want to write motor control software then you have little choice but to empirically measure what the startup power requirement is for your system and then add some more for margin. And hope that you added enough.
It seems to me that what you need is a voltage snubber across the MOSFET. An easy way to do that is to simply connect a series capacitor + resistor across the MOSFET. I'd guesstimate that a value of about 2.7 nF (about 3x capacitance of the MOSFET) and resistor of 100 \$\Omega\$ would be about right.
This ancient application note describes the various kinds of snubber circuits, including when and how to use them. You might find some inspiration there.
Best Answer
Yes, this is very different. PWM drive and voltage drive separately don't really mean that much, but when combined in this way you will get significantly different performance.
Electrically, you can model a motor as an inductor (windings), resistor and a voltage source (the EMF, proportional to the motor speed). When you apply a lower voltage compared to a higher voltage, you will:
With PWM and a higher voltage, you will be able to achieve higher peak speeds and often much higher torque at equal speeds.
There is no real reason that a motor will damage when applying higher voltages. Motor damage is caused by:
Also, overheating or running a motor at very high currents will cause a (significant) reduction in torque because of magnetic saturation.
If you can guarantee that you keep your motor within speed, torque and force limits as well as properly cool it, there is no downside to running it at higher voltages with PWM.