Problems deciphering fepout

From: Christopher Hartshorn (cmhartshorn_at_wsu.edu)
Date: Fri Jan 16 2009 - 16:28:21 CST

Hello. I am having trouble deciphering the output from the fep
calculations of NAMD. Briefly, I am performing the calculation to
measure dimerization of two proteins. Where I have two separate
systems already equilibrated, etc. One of which contains the
dimerized protein and the other sim has the two monomers separated in
space. Both in the same solvent system, etc. I have chosen to fade
one 1/2 of the dimerized protein out (columnB=-1) in the one sim and
fade one of the monomers out (column B=-1) in the other sim. I am
using the fep parameters from below and I am not sure of my out file's
values.

1) Do the dG's for each step always change w.r.t. the Lambda step?
As an example, one step in my calculation (0.3-->0.4) starts with
-15KCal/mol and ends (after 15000 steps) with -30KCal/mol this is the
case for all other Lambda steps. I ask because I thought that these
values would not change much (e.g. would vary slightly about some
constant value) because they were direct measurements done thousands
of times over to get a good sampling.

2) What is plotted when I look at the tutorials on FEP? I see that
it is dG vs. Lambda (0-->1), but where are the dG's coming from for
each Lambda step in this graph? Is it the -62 or -29 value from my
example here:
  (#Free energy change for lambda window [ 0.4 0.5 ] is -29.3926 ; net
change until now is -62.3803)?

source fep.tcl
fep on
fepFile dimer.fep
fepCol B
fepOutFile dimer.fepout
fepOutFreq 10
# LOOP OVER LAMBDA-STATES
fepEquilSteps 1500
set nSteps 15000
set dLambda 0.1
set init {0.0 0.000001 0.00001 0.0001 0.001 0.01 0.05
0.1}
set end {0.9 0.95 0.99 0.999 0.9999 0.99999 0.999999
1.0}
runFEPlist $init $nSteps
runFEP 0.1 0.9 $dLambda $nSteps
runFEPlist $end $nSteps

Thank you for any time you have to help.

Chris Hartshorn
WSU

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