VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Apr 26 2011 - 10:50:18 CDT

Ada,
  Chris Chipot's group has made some updates and/or bug fixes for the
parseFEP plugin, so if you like, I could send you the newest version
for you to try. Let me know if you're interested in this.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Apr 22, 2011 at 01:50:57PM -0600, Ada Zhan wrote:
> 'domain error' still appear after I tried the following things:
> 1) use equally spaced windows 0.5/-0.5 for forward/backward. (actually I
> tested the plugin using FEP tutorial sample output files)
> 2) use my own FEPout files, with increased no. of windows at ends.
> (FEPlist)
> the analysis can only go through 2 or 3 windows till the error massage
> comes out.
> And no graph pop out. (I have grace installed)
>
> Does anyone have an explanation?
> Thanks!
>
> Ada
>
> ______________________________________
> > From: Chris Chipot [chipot_at_ks.uiuc.edu]
> > Sent: Thursday, March 17, 2011 6:09 PM
> > To: Christian Jorgensen
> > Cc: namd-l_at_ks.uiuc.edu
> > Subject: Re: namd-l: New NAMD version 2011-03-03 uses
> >
> > Hi Christian,
> >
> > parseFEP assumes that the backward fepout file is the mirror image of
> the
> > forward fepout file, i.e. if in your forward file, you ran from I>> = 0
> to
> > 0.2, then
> > the backward file should range from I>> = 0.2 to 0. It also assumes that
> your
> > increment, I'I>>, is the same for the forward and backward
> transformations.
> >
> > Cheers,
> >
> > Chris Chipot
> >
> >
> > On 3/17/11 12:58 PM, Christian Jorgensen wrote:
> >> Hi all,
> >>
> >> when using ParseFEP with a fepout file for the forward and the backward
> run
> >> I keep encountering a domain error of the form
> >>
> >> 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 $w invoke]"
> >> (procedure "tk::ButtonUp" line 22)
> >> invoked from within
> >> "tk::ButtonUp .parseFEP.runbutton"
> >> (command bound to event)
> >>
> >>
> >>
> >> Does this invalid argument arising when calculating
> sqrt($instant_error_gauss) occur because $instant_error_gauss is taking
> values<0?
> >> I believe it is causing me issues because the ParseFEP log file stops
> at I>>=0.5
> >>
> >>
> >>
> >> #=================================================
> >> # Free energy perturbation
> >> # --------------------------------
> >> #forward/backward I>> a**a**A a**A
> I'Iu
> >> #
> >> #-------------------------------------------------
> >> forward: 0.0000 0.0000 0.0000
> 0.0000
> >> forward: 0.1000 -0.9392 -0.9392
> 0.0506
> >> forward: 0.2000 -0.8597 -1.7989
> 0.1287
> >> forward: 0.3000 -0.5557 -2.3547
> 0.1357
> >> forward: 0.4000 -0.5542 -2.9089
> 0.1381
> >> forward: 0.5000 -0.4808 -3.3897
> 0.1421
> >>
> >>
> >> Any input here would be really helpful
> >> thanks
> >> Christian
> >>
> >>
> >> ______
>
> --
> Chris Harrison, Ph.D.
> Theoretical and Computational Biophysics Group
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
> char_at_ks.uiuc.edu Voice: 217-244-1733
> http://www.ks.uiuc.edu/~char Fax: 217-244-6078 

-- 
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