For protein kinases, how long simulation is required to see the conformation change from DFG-in to DFG-out?

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Ramin Ekhteiari Salmas

If I'm not wrong, it may take at least 1 millisecond. You can try with accelerated MD simulations or umbrella sampling if you are aware of the activation pathway.

Krishnendu Bera

I'm agree with Ramin. You should do enhance sampling like metadynamics/SMD/umbrella sampling etc. It's difficult to predict the time scale in classical simulation before doing it. You may get your desire results within nano seconds or microseconds.

Sudhir Raghavan

Will you be doing the simulation in the presence of a ligand or inhibitor?

Rajiv Lakkaniga

No ligand/inhibitor. Just the protein.