I simulated three phase rectifier using a thyristor like so:
I get the expected result. But if I change the thyristors to IGBTs as shown below, it does not work.
Why do these two circuits behave differently?
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IGBTs and SCRs behave completely differently.
SCRs block cathode-to-anode, and conduct anode-to-cathode when gated and forward biased.
IGBTs with antiparallel diodes conduct emitter to collector, block collector to emitter unless gated, and conduct collector to emitter when gated.
In your case, you're turning on the upper and lower IGBTs at the same time. This causes a short circuit across the DC bus, which will break something. It will definitely not rectify. If you were not turning on the IGBTs, the circuit would behave like a normal diode rectifier. SCRs don't have that problem, because even when gated on they don't reverse-conduct. (It's still not a great idea to gate them on when heavily reverse-biased though.)
I'd give you other recommendations, if you could describe what goal you are trying to achieve.