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If using a 2mm thick thermal pad to connect the CPU to the heatsink, does the size of the pad matter? Should it be cut to the size of just the metal piece in the middle of the CPU (10mm x 10mm) or does it need to be sized for the entire CPU (25mm x 25mm) (i.e. including the green bit).

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It would just be for the metal areas.

Follow these guidelines to install a heatsink on a processor, using a thermal pad as the thermal interface material. Thermal pads should be used with AMD Athlon MP, AMD Athlon XP and AMD Duron processors only. These processors are lidless, that is, the processor die comes into direct contact with the heatsink.

  1. Verify that the heatsink has a thermal pad attached. If the heatsink does not have a thermal pad attached, locate the area of the heatsink that will directly contact the processor, and apply the thermal pad to this area only.
  2. Remove the protective film(s) from the thermal pad.
  3. Mount the heatsink onto the processor.

Always follow the AMD-recommended procedures to install a heatsink onto a processor to avoid damaging the processor or motherboard. See the Socket A AMD Processor and Heatsink Installation Guide, order# 23986 Do not re-use thermal pads. Before re-using the heatsink remove the thermal interface material and reapply a new thermal pad.

I highly suggest using thermal paste for capped processors though, it provides better conduction and paste life. This research paper from AMD has good instructions for both methods, as well as advantages and disadvantages.

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Given that thermal pads don't technically 'stick' to a component like thermal paste does, that would imply that the CPU can be changed without changing the thermal pad yes? Assuming stick side of the pad is stuck to the heatsink. –  Nicholas May 27 '11 at 2:02
    
You need to put down a new pad with each CPU change. Phase-change thermal pads melt when the CPU is in use. Over time, it tends to stick to the CPU and the heatsink. I did a research project with thermal interface material, and I could never get a CPU off without breaking the phase-change pad. –  Chris Ting May 27 '11 at 6:26
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I would personally recommend using thermal paste, two of my favourites are:

  • Arctic Cooling MX-2
  • Arctic Silver 5

Using a small blob smoothen it out with a cut piece of card and make the application a thin layer over the processer lid, there should be just enough that it covers an even film across.

Thermal Pads provide a thick layer increasing heat and are only recommended for components like Memory

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This application is for an embedded PC where the processor's heatsink is a solid internal extrusion of the outer casing (alluminium). We are using a think thermal pad to absorb any minor pressure or vibration that might be exhibited from the casing. –  Nicholas May 27 '11 at 1:33
    
@ Nicholas, Thermal pads are used by the PC industry for ease of assembly, low risk of an improper assembly, that being said "thermal paste" is the way to go when doing your own work on the heatsink. –  Moab May 27 '11 at 3:28
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Most of the heat will be coming from the metal section, but I'd cut the pad for the full size of the CPU package. The larger the heat transfer area the more heat you'll get out.

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My concern is that if the pad conducts heat, it will do so evenly over the entire pad area. Meaning that a larger pad would spread the heat evenly across the whole chip. Whereas a smaller pad would only duct the heat from the metal section and not spread the heat to the green section. –  Nicholas May 27 '11 at 1:36
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