Parse Fep plugin error

From: Joseph Antoine Garate (
Date: Fri Dec 23 2011 - 08:27:39 CST

Dear VMD developers:

I am starting to run some FEP calculations using NAMD, thus, I went over the Fep tutorial which I finished successfully. As a final step, I wanted to estimate the free energies errors (BAR estimator) by using the parsefep plugin (v1.4) of VMD , nevertheless there is a consistent error, (even when I use the output files provided by the tutorial). As you have explained in the VMD mailing list, this "bug" is related to a numerical error due to the "non-gaussianes" of the DeltaU distributions (if I understood properly). Maybe the simulations for the tutorial are really short, thus not providing a good estimation for the deltaU distribution, and there would be no bug if I simulate for longer times, nevertheless I have some questions:

Is this a bug or just a problem with the data provided to the program? By reading at the vmd-mail list, there is a newer version of this plugin, could someone provide this to me please?

Is this new version available at the CVS version of VMD?

Thanks in adavance




As reported by other users the error that I get is:

domain error: argument not in valid range
domain error: argument not in valid range
    while executing
"expr sqrt($instant_error_gauss) "
    (procedure "::ParseFEP::FEP_formula" line 361)
    invoked from within
"::ParseFEP::FEP_formula $file$file_entropy $file_lambda $window $mean_xi $fororback"
    (procedure "::ParseFEP::normal_parse_log" line 60)
    invoked from within
"::ParseFEP::normal_parse_log $::ParseFEP::fepofile forward "
    (procedure "::ParseFEP::namdparse" line 172)
    invoked from within
    (in namespace inscope "::ParseFEP" script line 21)
    invoked from within
"::namespace inscope ::ParseFEP {
##if {$::ParseFEP::fepbofile != ""} {set ::ParseFEP::sosindex 1 }

if { [string length $fepofile] < 1 } {
    invoked from within
".parseFEP.runbutton invoke"
    ("uplevel" body line 1)
    invoked from within
"uplevel #0 [list $w invoke]"
    (procedure "tk::ButtonUp" line 22)
    invoked from within
"tk::ButtonUp .parseFEP.runbutton"
    (command bound to event)

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