Dear Gmx Users, I am wondering your approach for such system:
Ligand binding alpha helix which is a part of big helical bundle - in reality the conformation is rather stable. I want to use position restrained dynamics - surely for terminal residues and possibly for the residue in the middle? (the lenght is app 9 nm). I want to avoid folding. What is your opinion? I want to perform this simulation as a starting point for binding free energy simulations via Umbrella Sampling then. I will have experimental validation via ITC. Please, let me know your opinion. Steven
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