This might sound a bit silly but most Video Card have many video output ports in the back, others have two DVI. For example, on my HD5870 Does it matter if I connect the DVI cable to the 1st or 2nd DVI port of the video card (this is when using single monitor only). Does it have an impact of the FPS of games?
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For the 5870, it does not matter which DVI port you connect the monitor if you have resolution of 1920x1080 or lower.
If you have monitor resolution >1920x1080, then you must use the DVI-Dual for best results.
Does it have an impact on the FPS of games if I am using the 1st DVI or 2nd DVI or HDMI port?
No, it should not have any impact whichever you use.
From a performance point of view, no difference. If you have two monitors attached, one of them will become the boot or bios display monitor. If you care which is which, connect , or exchange them accordingly.