From: Francesco Pietra (
Date: Mon Mar 05 2018 - 14:17:56 CST

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.


---------- Forwarded message ----------
From: Francesco Pietra <>
Date: Sat, Mar 3, 2018 at 6:44 PM
Subject: Fwd: parseFEP domain error
To: VMD Mailing List <>, NAMD <>

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 <>
Date: Fri, Mar 2, 2018 at 4:47 PM
Subject: parseFEP domain error
To: VMD Mailing List <>,

With frwd.fepout parseFEP invokes imagemagick, providing graphics besides

With frwd.fepout + back.fepout imagemagic only provides

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
    (procedure "::ParseFEP::normal_parse_log" line 55)
    invoked from within
"::ParseFEP::normal_parse_log $::ParseFEP::fepbofile backward "
    (procedure "namdparse" line 158)
    invoked from within
    (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
francesco_at_vaio64:~$ which compare
francesco_at_vaio64:~$ which composite
francesco_at_vaio64:~$ which conjure
francesco_at_vaio64:~$ which convert
francesco_at_vaio64:~$ which display
francesco_at_vaio64:~$ which identify
francesco_at_vaio64:~$ which import
francesco_at_vaio64:~$ which mogrify
francesco_at_vaio64:~$ which montage
francesco_at_vaio64:~$ which 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

Thanks for advice
francesco pietra