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 !
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