Re: vmd-l: Parse Fep plugin error

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Dec 23 2011 - 10:47:56 CST

Dear Antoine,
  Please give the current version of the Chipot group's parsefep plugin a spin
and let us know if you still encounter any problems. The new plugin is indeed
available in CVS, along with current versions of all of the other plugins.
I've attached the current version of parsefep.tcl to this email. You can replace
the one in your VMD with this one and try it out.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Dec 23, 2011 at 03:27:39PM +0100, Joseph Antoine Garate wrote:
> 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 By reading at the vmd-mail list, there is a newer version of this plugin, could someone provide this to me please?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
>
>
> Antoine
>
>
>
>
>
> P.S.
>
>
> 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 $::ParseFEP::fepofile forward "
> (procedure "::ParseFEP::namdparse" line 172)
> invoked from within
> "::ParseFEP::namdparse"
> (in namespace inscope "::ParseFEP" script line 21)
> invoked from within
> "::namespace inscope ::ParseFEP {
> ##if {$::ParseFEP::fepbofile != ""} {set ::ParseFEP::sosindex 1 }
>
>
> if { [string length $fepofile] < 1 } {
> tk_dial..."
> 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)
>
>
>
>
>

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078

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