setting configuration file for free energy perturbation

From: Deborah Jameson (
Date: Mon Jul 18 2005 - 10:25:02 CDT

I wanted to do simulation for computing free energy perturbation in NAMD .
I got the error message "Setting parameter fep file from script failed" after the 1000 step results for minimization .
The results for minimization period seems correct and the system is stable because the total energy change is neglegible.but the error appears just after thses minimization results.
It is mentionable that in configuration file I added the required fep parameters after minimization command.
structure myself.psf
coordinates myself.pdb
minimize 1000
reinitvels $temperature
fep on
fepfile rand.fep
fepCol B
fepOutFile rand.fepout
fepOutFreq 5
fepEquilSteps 3200
set step 0
set dstep 0.025
dlambda $dstep
while {$step < 1} {
firsttimestep 0
lambda $step
set step [expr $step+$dstep]
lambda2 $step
run 6400
Also, I want to ask about the difference between fepEquilSteps and run manual it is mentioned that in each window the esystem is equilibrated in 3200 steps before 6400 steps of data collection.if anybody help me on this problems and explain me more on the process of fep calculation,I will be very thankful.
Deborah Jameson

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