[gmx-users] how to simulate the transformation of loop

aixintiankong aixintiankong at 126.com
Wed Apr 17 03:15:55 CEST 2013

       In my system ,the loop is  part of the active pocket  of the protein. when the ligand is absent, the loop is disordered and if the ligand is present , the loop can transform into helix. i don't know how to the simulate the state of the shape of the loop at the different the situation. During the simulation, should i set  the specific parameters in the mdp , such as temperature or the others
      please give me some advice .thank you !

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