By default, the Gazebo graphical user interface will start full screen. It is possible to change this behavior. Try resizing and moving the main window. Then select File->Save Configuration. The next time Gazebo starts, the window position and size will be restored.
The position and size information is stored in a file called ~/.gazebo/gui.ini. You can manually modify this file by adjusting or adding the following lines:
Gazebo Issue #622: Joint velocities are high when the joint link is in contact and the joint is not rotating
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