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

[aixintiankong]

Dear,
       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 !