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It is said that it takes 200 hours for thermal paste to actually apply itself and truly do the job...

If this is the case, does it mean that my machine will gradually get cooler and cooler, the longer the thermal paste is on the heatsink (up to a point)?

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You might see a slight decrease in temperature as your paste sets in, but it isn't going to be anything drastic... a degree or two at most. Remember, the only reason we use thermal paste is because the two surfaces we are mating are not perfectly flat. Thermal paste fills in the microscopic pits on the surface of the processor and the heatsink effectively increasing the contact area between the two. In the first 200 hours of operation the thermal paste has been heated long enough "seep" into the microscopic nooks and crannies of the mating surfaces. Think of pouring hot syrup on your pancakes versus pouring cold syrup on your pancakes. The hot syrup spreads out and even soaks into the pancakes pretty well while the cold syrup stays in a tightly confined puddle and does not penetrate the pancakes very well at all.

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+1 - It's also important to only use a tiny bit of paste for this reason, as it should only be filling the tiny pits in the surfaces and not stopping them from making as much contact with eachother as possible. Heavy overclockers often do not use any thermal paste at all, after 'lapping' the surfaces. google.co.uk/… – paradroid Nov 17 '10 at 5:38
Follow the vendor's instructions as to how much paste you use (if you ever need to). It depends a lot on it's constituents and how much pressure/heat it requires to make it spread out. Using a "tiny" blob of something like Noctua NT-H1 will result in a cooked chip. I normally settle for an overnight burn-in as it checks the chip is running cool and allows the paste to spread under a constant load. – Tog Nov 17 '10 at 8:13
+1 and accepted answer...thanks! – studiohack♦ Nov 17 '10 at 16:55
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First for the 200 hours statement: It depends on type of thermal paste. There are pastes like Arctic Silver which need time to settle and there are thermal pastes like generic silicon based or Arctic Cooling MX-3 which do not need to settle.

Next point is about the way paste settles. It's not just the time itself that's needed. Volume of thermal paste changes with temperature. As it changes, paste starts to move into surfaces and fills irregularities. As it cools, it starts to move back to its starting position. That is why it is important to turn computer on and have it running for a while and then turn it off and have it cool for a time while the paste is settling.

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