VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri May 09 2008 - 02:29:22 CDT

Hi,
  I think that in order to run VMD in your PBS job script
you're going to want to do something more like this:
  ./vmd -dispdev text -eofexit < run.vmd > out

Try that and let us know if that cures your problem.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, May 06, 2008 at 03:40:44PM -0400, zhenlong li wrote:
> Hello everyone,
>
> To run vmd as pbs batch job, I used the pbs script as:
> #!/bin/sh
> #PBS -l walltime=300:00:00
> #PBS -l nodes=1:ppn=1
> #PBS -N m5810
>
> cd $HOME/vmd
> ./vmd -dispdev none -e run.vmd > out
>
> inside the run.vmd script:
>
> source bigdcd.tcl
> source micelle.tcl
> mol load psf 23810.psf
> bigdcd micelle 58105511.dcd
>
> inside the micelle.tcl,
> there is an output file where the results are dumped frame by frame:
>
> set fa1 [open micellenum.dat w]
> set fa2 [open micellelist.dat w]
>
> proc micelle {frame} {
> ..................
> puts $fa1 "$frame $core8_num_agg $mwn
> $mww "
> ..................
> }
>
> (I am not sure yet where to close this file automatically after all the
> frames are looped )
>
> If I run the commands in the run.vmd file in the vmd console, it works. But
> when the job is submitted as above, the job stop immediately. I guess there
> is
> sth wrong with the running levels of this pbs job.
> Anybody gives me a hint please? thanks a lot!
>
> best regards
> Zhenlong
>
> --
> Zhenlong 

-- 
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