I have a ASUS Z97 Pro Mobo and a Corsair H60 cooler.
The H60 cooler has two pins; one for the pump and one for the fan. Is it okay to put the fan in the CPU Fan connector and the pump in the CPU Opt connector?
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Yes, though it's a good idea to go into the bios and make sure things like 'cool n quiet' or whatever automatic fan controls are equipped on your motherboard are turned off. You'll want steady power to the pump to keep the coolant moving.