From: Sting (stg1979_at_emails.bjut.edu.cn)
Date: Mon Jun 18 2007 - 23:00:38 CDT
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 try to reconstruct the PMF, and I have some problem as follow:
1. How to compute the works done during the process? Should it be: The displacement of ligand*applied Force or The displacement of the moving point which drag the ligand ?
2. What is the diffrence between the PMF and the Activation Energy as well as that between it and the Free Energy of Activation, and how to verify a reasonable PMF?
I really need someone to help me. Thank you in advance!
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