From: Debaditya Mukherjee (debadityam7_at_gmail.com)
Date: Fri Mar 10 2017 - 23:40:50 CST
Hi all NAMD users,
I performed an alchemical FEP for mutation of Alanine to Threonine, and got
a Forward free energy change of +0.63 and backward free energy change of
+0.60. When i used ParseFEP plugin in VMD to calculate the total free
energy change , it came as 0.295 and total error of 0.047. I have few
questions regarding these observations:-
q1. why mutation of A-T giving free energy change of almost 0?
q2. How come the forward and backward values have the same sign (positive)?
q3. How is this total error calculated?
q4. How can the total free energy change through ParseFEP be 0.295, not
matching with the average?
Can anyone please help me to solve it?
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