[gmx-users] how to describe the change of channel in the MD

[aixintiankong]

 Dear,
     In the MD, I find that when the ligand keep in the active site , the 
channel formed by two loops is closed. without the ligand the channel is 
opened. I don't know how to describe the change of channel. could i describe 
the channel by calculating the the most narrow distance(mass center) between 
the residues on the two loops? please give me some adviece. thank you very much!
   
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