Re: Fwd: parseFEP domain error

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Mar 07 2018 - 08:39:49 CST

Hi Chris:
Thanks for your mail. I was familiar with namd nightly build, while I was
unable to locate a nightly build 1.9.3 vmd. The prerelease 1.9.4 is also
dated to 2017.

with my best regards
francesco

On Tue, Mar 6, 2018 at 12:25 AM, Chris Chipot <chipot_at_ks.uiuc.edu> wrote:

> Hello Francesco,
>
> thank you for your message and for pointing this issue to our attention.
> ParseFEP has undergone a number of important changes recently, and in the
> process, the link to XMGrace and ImageMagick has been broken. Sorry for the
> trouble it has created. The problem has now been fixed, and a revised
> version of the code should be available in the next nightly build of VMD.
>
> Cheers,
>
> Chris Chipot
>
>
>
> On 3/6/18 5:17 AM, Francesco Pietra wrote:
>
> At this point, I would appreciate very much receiving frwd.fepout and
> back.fepout couple of files from whatever system. Just to check whether
> there is anything wrong with grace/imagemgick from debian amd64, or with
> namd creating those .fepout for my system.
>
> Thanks
>
> francesco
> ---------- Forwarded message ----------
> From: Francesco Pietra <chiendarret_at_gmail.com>
> Date: Sat, Mar 3, 2018 at 6:44 PM
> Subject: Fwd: parseFEP domain error
> To: VMD Mailing List <vmd-l_at_ks.uiuc.edu>, NAMD <namd-l_at_ks.uiuc.edu>
>
>
> Hello
> As, in my hands, parseFEP fails to call imagemagick when both frwd and
> back PEF are submitted (while it works when frwd alone is submitted), is
> there any described way to reconstruct from the log files all graphics ?
> From what I could do to this regard, grace plots from ParseFep. do match.
>
> Thanks for help
>
> francesco pietra
>
> ---------- Forwarded message ----------
> From: Francesco Pietra <chiendarret_at_gmail.com>
> Date: Fri, Mar 2, 2018 at 4:47 PM
> Subject: parseFEP domain error
> To: VMD Mailing List <vmd-l_at_ks.uiuc.edu>, namd_at_ks.uiuc.edu
>
>
> Hello:
> With frwd.fepout parseFEP invokes imagemagick, providing graphics besides
> tables.
>
> With frwd.fepout + back.fepout imagemagic only provides
> entropy.log
> gc.log
> ParseFEP.log
>
> not invoking imagemagick, while reporting the error:
> domain error: argument not in valid range
> domain error: argument not in valid range
> while executing
> "expr $nSample * $var / ($sigma_factor ** 2) "
> (procedure "::ParseFEP::FEP_formula" line 95)
> invoked from within
> "::ParseFEP::FEP_formula $file $file_entropy $window $mean_xi
> $fororback"
> (procedure "::ParseFEP::normal_parse_log" line 55)
> invoked from within
> "::ParseFEP::normal_parse_log $::ParseFEP::fepbofile backward "
> (procedure "namdparse" line 158)
> invoked from within
> "namdparse"
> (in namespace inscope "::ParseFEP" script line 16)
> invoked from within
> "::namespace inscope ::ParseFEP {
>
> if { [string length $::ParseFEP::fepofile] < 1 } {
> tk_dialog .errmsg {NamdPlot Error} "No FEP (inward) logfile
> ..."
> invoked from within
> ".parseFEP.runbutton invoke"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list $w invoke]"
> (procedure "tk::ButtonUp" line 22)
> invoked from within
> "tk::ButtonUp .parseFEP.runbutton"
> (command bound to event)
>
> SOFTWARE USED: VMD 1.9.3 on debian 9 (stretch) amd64 with XFCE
>
> all imagemagic programs are on the path:
> francesco_at_vaio64:~$ which animate
> /usr/bin/animate
> francesco_at_vaio64:~$ which compare
> /usr/bin/compare
> francesco_at_vaio64:~$ which composite
> /usr/bin/composite
> francesco_at_vaio64:~$ which conjure
> /usr/bin/conjure
> francesco_at_vaio64:~$ which convert
> /usr/bin/convert
> francesco_at_vaio64:~$ which display
> /usr/bin/display
> francesco_at_vaio64:~$ which identify
> /usr/bin/identify
> francesco_at_vaio64:~$ which import
> /usr/bin/import
> francesco_at_vaio64:~$ which mogrify
> /usr/bin/mogrify
> francesco_at_vaio64:~$ which montage
> /usr/bin/montage
> francesco_at_vaio64:~$ which stream
> /usr/bin/stream
>
> Incidentally, I was surprised that the following command ($ or #) did not
> show /usr/bin with the various programs
> francesco_at_vaio64:~$ dpkg -L imagemagick
> /.
> /usr
> /usr/share
> /usr/share/bug
> /usr/share/doc
> /usr/share/doc/imagemagick
> /usr/share/doc/imagemagick/NEWS.Debian.gz
> /usr/share/doc/imagemagick/changelog.Debian.gz
> /usr/share/doc/imagemagick/changelog.gz
> /usr/share/doc/imagemagick/copyright
> /usr/share/bug/imagemagick
>
>
> Thanks for advice
> francesco pietra
>
>
>
>
>
> --
>
> Chris Chipot
> CNRS research director, University of Lorraine
> Adjunct professor of physics, University of Illinois, Urbana-Champaign
>
> _______________________________________________________________________
>
> Chris Chipot, Ph.D.
> Theoretical and Computational Biophysics Group
> 3165 Beckman Institute for Advanced Science and Technology
> University of Illinois at Urbana-Champaign
> 405 North Mathews
> Urbana, Illinois 61801 Phone: (217) 300-0380
>
> E-mail: chipot_at_ks.uiuc.edu
> Christophe.Chipot_at_Univ-Lorraine.fr
> Web: http://www.ks.uiuc.edu/~chipot
> http://www.lia-uiuc.cnrs.fr
>
> It is hard for France to maintain a thirty-five-hour workweek when
> China and India have invented a thirty-five-hour workday.
> Thomas L. Friedman
> _______________________________________________________________________
>
>

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