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A have a 500GB Transcend StoreJet which turns off after a while when it's not in use. The hard drive runs perfectly though - no issues.

It can't be related to my USB ports since my other external HDDs run fine all the time, except this one when it's not in use. If I unplug the USB and plug it back in, it works fine until it's not in use.

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... and your question is? –  David Schwartz Apr 10 '12 at 20:45
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up vote 2 down vote accepted

This feature is called by marketing "green" or "smart" or "Independent Power Management", and it puts the HDD to sleep when not in use. It can be removed using firmware tools from the manufacturer.

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Should be able to some how disable it under the Drive properties in my computer, possibly.. –  ekaj Apr 10 '12 at 20:56
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It depends on the drivers and OS... Better cut the feature from its root. :) –  Radoo Apr 10 '12 at 20:59
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Some drives cannot be changed and will always power down. –  Dave M Apr 10 '12 at 22:06
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Have you looked at your Power Options within Windows to disable the drive spindown when idle after a certain amount of time?

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