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The only way a hard drive can bottle neck gaming is with your loading times, but it doesn't actually affect performance, you just might spend a little longer sitting on the loading screens.
Also when it comes to speeds with mechanical hard drives it's proportional to how much stuff you have on the hard drive. A hard drive that is almost full runs slower than a hard drive that is empty. What I would do is install the OS on the WD 1TB hard drive, since it is faster have games on that, but all movies and music on the 500GB drive, but honestly it won't make much difference at all.
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