convergence of FEP calculation.

From: dbaogen (dbaogen_at_gmail.com)
Date: Mon Dec 10 2012 - 21:16:09 CST

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Dear all,

           I want to calculate the relative free energy difference between ATP (GTP) and protein using FEP method. But in the course of calculation, the forward and backward analysis can not overlap like the example shown in FEP_tutorials which downloaded from the website. Is it to shown that the FEP analysis in my studied system is not convergent? The following "FEP parameters" are set for the free ATP (GTP) molecule in water solution:

source ./fep.tcl

alch on
alchType FEP
alchFile ion_solv.fep
alchCol B
alchOutFile forward-on.fepout
alchOutFreq 10

alchVdwLambdaEnd 1.0
alchElecLambdaStart 0.5
alchVdWShiftCoeff 4.0
alchDecouple on

alchEquilSteps 500
set numSteps 2000

runFEP 0.0 1.0 0.003125 $numSteps

Among the above FEP parameters, which are important and will influence the convergence? Thanks!

Best wishes
Duan Baogen

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