VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sat Mar 03 2018 - 11:44:06 CST

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