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Alright I'm at work I'll have to un SLI it tonight I guess I should just put my 4870 1GB in there instead of having it sit on my desk doing nothing! How will it fold compared to my BFG 8800 GT OC2 512MB
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Your 8800GT will probably fold better than the 4870. The nVidia kicks butt in folding. Don't put both ATI and nVidia in the same rig (I was warned multiple times not to do this myself when I asked).
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(did have these in SLI but appears since I'm using Vista 64 you guys think I have to unlink the SLI)?
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You have to unlink the SLI or Crossfire unfortunately.
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BTW is it wise to run the CPU and GPU f@h at the same time on one machine (just use different Machine ID's?
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Yes. You can use both at once. You are correct also about having different machine IDs too, so you are learning fine.

In the advanced panel for F@H, you might want to set the GPU client to slightly higher, and the CPU one to slightly lower.
However, there is a catch; CPU folding@home is not very efficient. Get those GPU clients up and running properly first, and then we can talk about folding using the vmware client, which will get you way more points per day.