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For the fun of it I decided to let nTune 5 find the best overclocks for my system. For the most part it seemed to work okay but I'm wondering why does it insist on raising my agp/pci bus speed? Isn't that a dangerous thing to do or is it assuming if your system passed the 3 hour stress test it won't harm it. Also, what gain would you even have from overclocking the pci bus?

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The PCI/AGP bus speeds are supposed to be linked to your FSB. However, PCI/AGP busses don't like being overclocked, just because you passed a three hour stress test doesn't make the components on those busses more likely to like an overclocked bus. The only gain I could think of would be getting more bandwidth (more mhz), but that doesn't work because peripherals don't like being overclocked.

People used to kill off network cards and corrupt their data.

They're link on the board. Boards keep a certain ratio between the FSB/AGP/PCI, not sure as to why...someone better informed can probably explain, or I can look it up later..

They're usually linked anyway, I don't know how nTune works as I do everything in the BIOS.

I would honestly avoid using nTune... a lot of the settings it picks are just ridiculous and are far from optimal. Often the settings it picks overshoot the mark and are very unstable (it has all sorts of problems with FSB/PCI locks). Take some time and read lots of overclocking guides - it will involve a lot of messing around in BIOS but it's worth it in the end. I started with nTune but got MUCH better results after reading around online. The advantage is that even if you reinstall Windows all your settings will still be there and working exactly the same as before.

actually you know what? I played with the program a little more and found that it's only the AGP bus it is increasing to 77. The PCI bus says it's at 33 so that is only applying to my video card then correct?

Your video card would be the only thing on the AGP bus, yes. I've heard of crazy stories of people getting better video cards oc's by increasing their PCI-E clocks, no idea if it's the same with AGP. However, it was rare and most people didn't get anything from oc'ing their PCI-E buses.

Theoretically, overclocking the PCI/AGP bus should make things a bit faster (just like PCIe x16 is faster than AGP 8x is faster than AGP 4x etc.), so by overclocking the AGP bus you're increasing the bandwidth between your system and your graphics card. The difference is usually negligible though, and I don't think it's worth it. The PCI/AGP bus is quite prone to corruption, so some of your devices like a sound card or of course graphics card might not work properly. That also includes devices integrated into the motherboard, like integrated sound, LAN, and most importantly your IDE/SATA controller. If the PCI bus is set too high, it might corrupt the data going to and from your hard drives. Anyways, I don't think nTune even supports any motherboards that don't have a PCI/AGP frequency lock (i.e. the PCI/AGP clock is independent of the FSB), so if nTune is increasing it, just lower it or overclock the "hard" way.

Also, yeah there are some graphics cards like the 7900GT that overclock better with the PCIe bus set a bit higher... I don't really know why either but I've tried it myself and it's true.

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