If you're looking to swap the Ctrl + Cmd keys in Ubuntu 16.04 either just because, or because you're using VirtualBox with an Ubuntu guest and an OSX host, then the answer you're looking for is here. Courtesy of Joel Koh.

Source

http://askubuntu.com/questions/131900/how-do-i-switch-the-command-key-and-control-key-on-a-macbook-pro

Instructions

1. Launch terminal
2. Edit X Keyboard Extension

nano /usr/share/X11/xkb/symbols/pc

3. Make the following changes. Ensure your file looks like this:

key <LCTL> {    [ Super_L       ]   };
key <LWIN> {    [ Control_L     ]   };
key <RCTL> {    [ Super_R       ]   };
key <RWIN> {    [ Control_R     ]   };

4. Clear xkb's cache

rm -rf /var/lib/xkb/*

5. (Conditional) If the keys are not swapped after step 4, restart your computer. It worked for me after this.

Hope it helps, good luck!