VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Feb 25 2010 - 16:46:08 CST

Hi,
  I'm not sure what's going wrong given the script you've got there,
but my suggestion would be to try running on a trivially small test case,
first running the steps by hand, and then chaining them together in a script
like the job script you had below. Once those work, I'd try it within
the queuing system and verify that everything still works there. Once
you've figured out what is going wrong (e.g. does bigDCD ever complete,
or does it get stuck? Does namdenergy get stuck?), then we can give
you more assistance.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Feb 24, 2010 at 05:21:34PM +0100, Andrea Carotti wrote:
> 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 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078