Dear Dr.Justin I had asked this question before but unfortunately I didn't answered good!
Instead of Pulling and separating some structures in definite distances, I located my drug in definite distances along z axis (as my initial structures for doing umbrella sampling). Am I right? The main problem underlying this question is : Do we need to know the velocity of drug in every structure we choose for doing umbrella sampling?(do they need to include the velocities too?) if no,which criteria assures with this K our molecule can cover the length of it's windows? Because I have chosen windows with different lingthes,And I want now to choose K so that it can sweep the lengthes. Thanks in advance for your reply
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