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

aixintiankong aixintiankong at 126.com
Wed Jun 19 17:21:28 CEST 2013

     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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