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From a HDD protection stand point, is it better to leave my desktop always on for the whole day, or is it better to let it Suspend/Standby after a given period of time (say 30 minute)?

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The hard drive spins down when the computer is idle for a certain time, whether you suspend the entire computer or not. Therefore, it shouldn't make any difference. – Dennis Oct 30 '12 at 16:28
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That depends on your usage.

The most harm is done to a drive by spinning up after suspend/standby. The less you do that the better. But leaving it running also slowly wears parts.

If you are going into standby every 5 minutes only to wake it up a few minutes later: leave it on.

If you have to choose between standby during the weekend or leaving it on it is probably best to go to standby.

I know that these are two extremes. But we have no idea what your average usage is.

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To add here, the hard drive won't spin down by itself when it's not used unless it's a drive that comes with that power saving feature (usually called "green drives") or the user configures the operating system to do so. – M K Oct 30 '12 at 17:06
    
Check. Most (all?) SATA drives come with this feature, but it is not always enabled. – Hennes Oct 30 '12 at 17:26
    
how can I check if my HDD support it or not? – Chin Oct 30 '12 at 18:22
    
That depends on the manufacturer, the model and even the firmware. Which means you either 1) hope you got a manual (for a HDD: unlikely these days), 2) google for the model or 3) Probe the drive with the windows variant of hdparms or 4) boot a live CD and try it with hdparms – Hennes Oct 30 '12 at 19:03

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