From: Dan Willenbring (dan_at_omitted.net)
Date: Sat Jan 17 2009 - 08:58:14 CST
Christopher,
An FEP calculation will only converge properly if the difference
between two states is small enough. This is why it is broken up into
many smaller windows. For an entire protein, you might try more
steps and/or smaller windows.
For the tutorial, I believe the plots are of the lambda value at the
end of each lambda window versus net change (in your example, you
would plot 0.5, -62.38..). You don't have it in your log file, but
you could add lambda 0.0, net change 0.0 when you make the plot.
Dan
On Jan 16, 2009, at 5:28 PM, Christopher Hartshorn wrote:
> 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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