From: Sting (stg1979_at_emails.bjut.edu.cn)
Date: Thu Jun 14 2007 - 21:49:03 CDT
I am confused about the diffrence between the PMF and the Activation Energy as well as that between it and the Free Energy of Activation.
I have performed a series of SMD with a constant velocity of 10 Å/ns to force a ligand release from the binding pocket and the the reconstructed PMF is about 100 kJ/mol. A reviewer of my paper considered that the obtained value is much too large and would prohibit any realease. But during our simulations, the maximum forces needed is only about 600 pN, which is commonly obtained in other's works, and the value of PMF we obtained is also similar to the other's work. How shoud I argue myself?
Any suggestion will realy be helpful!
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