VMD-L Mailing List

From: Ada Zhan (zyqfrog10_at_msn.com)
Date: Tue Apr 26 2011 - 15:02:24 CDT

Hi, John,

That would be wonderful! Please send it to me!
Thank you!

Ada
> Date: Tue, 26 Apr 2011 10:50:18 -0500
> From: johns_at_ks.uiuc.edu
> To: zyqfrog10_at_msn.com
> CC: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: ParseFEP_domain error
>
>
> 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