Re: vmd-l: Fwd: parseFEP domain error

From: Brian Radak (brian.radak_at_gmail.com)
Date: Mon Mar 05 2018 - 15:43:15 CST

I'm not a ParseFEP expert but I've worked with the developers a bit and
looked at the code some. There's usually a pretty graceful error if xmgrace
is not available on your computer and this doesn't look like it.

Looking at: "expr $nSample * $var / ($sigma_factor ** 2)" and "domain
error" makes me think there's a divide by zero error here, but I couldn't
say what sigma_factor is (I *think* the statistical inefficiency or
something similar?).

Here are some pretty good test files for an ethane <-> ethane null
transformation
https://www.dropbox.com/s/xxz2d56p54odk27/forw.test.fep?dl=0
https://www.dropbox.com/s/awi8obw7epqfiqs/back.test.fep?dl=0

HTH,
BKR

On Mon, Mar 5, 2018 at 3:17 PM, Francesco Pietra <chiendarret_at_gmail.com>
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
>
>
>
>

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