For each machine running xmodmap will give you the mapping and keycode, take a look first then write the script. I use ubuntu and mac keyboard. The below maps both left and right control and super.

Create an .Xmodmap file in your Linux home directory, with the following contents, then execute xmodmap .Xmodmap

clear control
clear mod4

keycode 37 = Super_L
keycode 105 = Super_R