question about relative binding free energy calculation method using FEP

From: dbaogen (
Date: Sat Nov 24 2012 - 05:58:55 CST

Dear all,

         I want to calculate the relative free energy between RAN polymerase and ATP or GTP using FEP method implemented in NAMD software. Firstly, the mutation of ATP to GTP in water solution is calculated. After 100 ps equilibrium of the system, forward and backward FEP analysis are carried out. The energy values are close when lambda value is larger than 0.5. But there exists deviation when lambda value is less than 0.5. what will result in this condition? The FEP parameter setting is as follow:
alchVdwLambdaEnd 1.0
alchElecLambdaStart 0.5
alchVdWShiftCoeff 4.0
alchDecouple on

        Another question is how to obtain the energy value when lambda is equal to 0 or 1 corresponding to forward or backward analysis? If the initial value of lambda is 0, and increment is 0.05. when the calculation is completed, the output *.fepout file will give the energy value from 0.5 to 1. Does the energy value correspond to lambda(0) state when I set the FEP parameters alchLambda (0 ) and alchLambda2 (0) simultaneously?
Would you like to help me with the problems? Thank you for your great help!

Best wishes

Duan Baogen

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