VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Sep 08 2006 - 16:32:18 CDT

Hi,
  Another way to do it is to use this modified version of bigdcd
(by Jordi and Leo) and call bigdcd_wait_till_done at the end of your script.
(see attachment)

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Sep 08, 2006 at 01:04:35PM -0400, Axel Kohlmeyer wrote:
> On 9/8/06, Hamsa Priya Mohana sundaram <mhamsapriya_at_gmail.com> 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.
>
> cheers,
> axel.
> >
> >Thanks
> >Hamsa
> >
> >
>
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> 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. 

-- 
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