Center-of-mass (COM)-center-of-mass (COM) distance between target and drug should be provided from MD simulation (distance vs time plot).
Annemarie Honegger
You can use the vmd (virtual molecular dynamics, http://www.ks.uiuc.edu/Research/vmd/ ) measure command.
see VMD User's guide ( https://www.ks.uiuc.edu/Research/vmd/current/ug/ug.html)
measure ( https://www.ks.uiuc.edu/Research/vmd/current/ug/node138.html )
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Norman Geist
You can use this VMD script to obtain the COM-COM distance between two selections and saved to a text file. Load you trajectory to VMD and source the script from the Extensions->Tk Console ;)
The resulting file can be plotted with e.g. xmgrace
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