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Yes another newb cooling question.:D I got a new 5.25 hard drive cooler that has 2 40mm intake fans. It says to mount the flat side of the hard drive to the aluminum cooling panel. Like CPU heatsinks should I use some thermal compond between the two or is that a bad idea?
You can do this but it takes a lot and the effects can be minor at best. Also, the drive surface is seldom flat so compound wouldn't help in those areas. We recommend that if you have a lot of flat area making contact with the heatsink to get some cheap metal based compound, you don't have to go for the expensive stuff (We personally use OCZ Ultra Silver because it's cheap and good for this application.) and spread a thin layer. But you will be fine if you decide not to do this. You may see a 1-2 degree drop by using compound. I give the effort because my gaming machine has a 15,000 rpm drive in it and I want to take no chances.
For one 7200RPM drive you don't really need to worry about it.