VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Feb 23 2006 - 16:31:10 CST

Hi,
  The call to exit may indeed be the source of your trouble.
You didn't specify how you're running VMD. Are you using the -eofexit
command line flag when you run it on your script remotely?
  http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.3/ug/node188.html

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Feb 23, 2006 at 10:05:09PM +0100, Nicolas Sapay wrote:
> Hello everybody,
> I'm using some TCL scripts to analyze a big trajectory. I call TCL procs
> in a VMD script. The TCL functions use bigdcd procedure to load and
> analyze the DCD file. So, my VMD script contains something like this:
>
> trace variable vmd_trajectory_read w zdistance_done
> big_zdistance -dcd $dcdfile -seltext1 "lipid" -seltext2 "protein" -step
> 10 -out $outfile
>
> And in the big_zdistance proc, there is:
> bigdcd get_zdist $dcdfile
>
> Fianlly, there is an "exit" command in the zdistance_done proc
>
> This works perfectly when I run my script locally. But when I run VMD
> through a Job server (PBSpro), 1 or 2 frames are loaded, and then VMD
> exits. Has someone ever met this kind of problem?
>
> Thanks
>
> Nicolas
>
>
> [ Dr Nicolas Sapay ]
> Institut de Biologie et Chimie des Protéines
> CNRS - Claude Bernard University, IFR128 Bioscience Lyon-Gerland
> Phone: +33 (0)4 72 72 26 46 - Fax: +33 (0)4 72 72 26 46
> Address: 7 passage du Vercors, 69367-F Lyon cedex 07, France
> 

-- 
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