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I've designed a simple non-inverting amplifier to interface a 3.3V MCU and a 5V signal to a motor controller. When I first tested with the MCU and the desired values to the low-pass filter, I noted that something was strange. This way, I decided to perform a test using the circuit below, where the PWM is from an Arduino.

circuit

The table below shows my results:

values

I tried swaping the PWM + filter for a 1k pot but the results were similar. I also tried swaping the multimeter and the op amp, nothing changes. Some tip why I'm having this behavior in this circuit?

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    \$\begingroup\$ If you're really using a TL082 as indicated in your schematic, that's that's your answer right there. It's not a "rail-to-rail" opamp. As your own measurements show, it can't get any closer than a couple of volts to either of its supply rails. \$\endgroup\$ – brhans Apr 6 at 23:25
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Not only can the TL082 output not swing to the negative rail, the input common mode range only starts 4V above the negative rail worst case (see datasheet).

You don't need a rail-to-rail op-amp but you do need a "single supply" op-amp or an op-amp with rail-to-rail input and output capable of handling your 12V supply (many modern op-amps are not able to handle such a high voltage).

For example, LM358 would work. Not the most accurate in the world, but quite usable, cheap as chips, relatively rugged electrically, and will easily give your 5V output with a 12V supply.

Note that amplifiers like the LM358 have a bias current which flows out of the input pin, so a floating GPIO pin will result in the op-amp output floating up towards the positive rail. If the pin is tristated and the driver chip is powered, it will likely exceed your 5V output. A 10K from the GPIO to ground would prevent that.

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enter image description here

*Figure 1. The TL082 datasheet shows that the output can only swing to within 1.5 to 2 V of the supply rails when on a ±15 V supply. On a single-ended 12 V supply it may be even worse.

You need an op-amp that can swing to the negative rail.

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