From: Axel Kohlmeyer (
Date: Fri Sep 08 2006 - 12:04:35 CDT

On 9/8/06, Hamsa Priya Mohana sundaram <> wrote:
> Hi all,
> I am trying to use bigdcd script for loading large dcd files for
> analysis in vmd.
> As a test run, i am trying to writedown box dimension from test.dcd
> containing 5 frames.
> When i run the tcl script (attached with this mail) in Linux: text mode the
> following way
> " > vmd -dispdev text
> vmd > source boxbig2.tcl "
> i am able to write down the box dimensions for all frames.
> However when i try to run it as a batch job, my output file contains only
> the dimensions
> corresponding to first frame. I used the following command in my PBS script
> for executing the tcl script
> "vmd -dispdev text -eofexit < boxbig2.tcl > box.log"
> Could anyone please tell me what is the mistake?

the problem is, that the bigdcd processing is done in the background
by hooking into the animate loop during reading of the trajectory
and deleting every frame as soon as it has been processed.

so once you start the analysis, the command prompt returns (or you'll
reach the end of file) and your batch job will exit.

as it is right now, you'll have to add a sufficiently large sleep
statement at the end your script, so your vmd session will not
terminate before the analysis is done.

many batch systems allow requesting interactive shells, so perhaps
running the analysis interactively, might be an alternative until we
found a better way of handling this.

> Thanks
> Hamsa

Axel Kohlmeyer
  Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.