how to cut off power from usb device using arduino
switching the ground wire of the usb modem on/off.


Bad choice. Use a P-channel MOSFET (like IRLML6401) to switch the +5 Volt wire instead.

Cutting GND could make the data lines float near the 5 Volts power level, because there is usually some ESD protection on them. There may also be some return current on them. Both would cause malfunctions in USB hubs. 


  how usb plug works, is first connect the power wire, wait some micro seconds


The reason behind this is to reduce the chance of ESD damage in the data lines - the power lines are much less likely damaged by ESD. You don't need to separate the data lines (and GND) at all if you just cut the power on the 5 volt line.