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Is there a way to support two different resolutions on my dual screens, one of 1600x900 and one 1200x1024?

Does it depend on my graphics card or is there third party software that can achieve this?

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What is your graphic card? Nvidia?

If you are using Nvidia graphic card, you can manage your displays using "Nvidia Xserver Settings" easily and graphical. Just open the application, go to "X Server Display Configuration". You can see your monitors here, just click on each you want to manage and then click advanced and change the resolutions parameter.

Another way is managing your screen resolutions by xorg.conf file. open the xorg.conf file and find the Section "Screen" ,under the SubSection "Display" add Modes "1024x768" "800x600".

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You can use xrandr to do this quickly and easily. xrandr can also find the resolutions for you. You can run xrandr with no flags to get a description of your current screens. For example, if you have a laptop you might have:

Screen 0: minimum 320 x 200, current 1366 x 768, maximum 8192 x 8192
LVDS1 connected 1366x768+0+0 (normal left inverted right x axis y axis) 277mm x 156mm
   1366x768      60.02*+
   1360x768      59.80    59.96  
   1024x768      60.00  
   800x600       60.32    56.25  
   640x480       59.94  
VGA1 disconnected (normal left inverted right x axis y axis)
HDMI1 disconnected (normal left inverted right x axis y axis)
DP1 disconnected (normal left inverted right x axis y axis)
HDMI2 disconnected (normal left inverted right x axis y axis)
HDMI3 disconnected (normal left inverted right x axis y axis)
DP2 disconnected (normal left inverted right x axis y axis)
DP3 disconnected (normal left inverted right x axis y axis)

If you plug in an external monitor to the VGA port and rerun xrandr you will see that the VGA section will get populated even if your system doesn't immediately start using the new display.

Using xrandr you can set the location and resolution of the two displays independently.

xrandr --output VGA1 --auto --right-of LVDS1

This will choose the resolution for the VGA monitor and extend your desktop to the right of your laptop's.

There are a number of other things you can do with xrandr. Arch has a good wiki on dual head setups.

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