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From: Andrea Carotti (andcar_at_chimfarm.unipg.it)
Date: Wed Feb 24 2010 - 10:21:34 CST
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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
- Next message: matziast_at_med.uth.gr: "about command measure dipole"
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- Next in thread: John Stone: "Re: Bigdcd and Namdenergy batch problem"
- Reply: John Stone: "Re: Bigdcd and Namdenergy batch problem"
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