VMD-L Mailing List

From: Andrea Carotti (andcar_at_chimfarm.unipg.it)
Date: Wed Feb 24 2010 - 10:21:34 CST

Hi all,

I'm trying to use bigdcd script for loading large dcd files and perform
namdenergy analysis with vmd. I'm trying to do this in batch mode, for
multiple large dcd files, as described into the bigdcd.tcl example 2
(http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/bigdcd/bigdcd.tcl).
 
For each dcd file I prepared a script as the one that follow

########################
source ~/bigdcd.tcl

source ~/namdenergy.tcl

set dcd "file_name.dcd"

set psf "file_namepsf"

proc NAMDENE { frame } {

set sel1 [atomselect top "serial A to B "]

set sel2 [atomselect top "serial C to D"]

set xsc "file_name.xsc"

namdenergy -vdw -elec -sel $sel1 $sel2 -par PARM.PRM -switch 8 -cutoff 12
-extsys $xsc -pme

}

mol load psf $psf ;#this gets the molid 0

bigdcd NAMDENE $dcd

bigdcd_wait

quit

##################################

Then I've generated an SGE queue submission script with multiple command lines like the
following

cd /working_directory/
~/vmd -dispdev text -e ~/script_for_dcd_file_like_below.tcl > output.txt
cd /working_directory2/
~/vmd -dispdev text -e ~/script_for_dcd_file_like_below2.tcl > output2.txt
......

When I submit this multiple-command-lines script (or even if I run it from the terminal as a shell script), I obtain
results only for the first dcd file, even if the job continues running without ending.
It seems that bigdcd.tcl is executed correctly once
(accordingly to the first command line of the second script), but probably
there is something wrong in the script and it is
unable to finish/exit to pass to the subsequent steps.

Briefly, my aim is performing iteratively namdenergy calculations for very
large dcd file using bigdcd.tcl script.
Is there someone who tried to do the same previously?
Am I missing something
Thanks in advance
Andrea 

-- 
ŻŻŻŻŻŻŻŻŻŻŻŻŻŻŻŻŻŻŻŻŻŻŻŻ
Andrea Carotti
Dipartimento di Chimica e Tecnologia del Farmaco
Università di Perugia
Via del Liceo, 1
06123 Perugia, Italy
phone: +39 075 585 5169
fax: +39 075 585 5161
www http://rpg.unipg.it
personal www http://iris.chimfarm.unipg.it/users/andcar