VMD-L Mailing List

From: nsapay_at_ibcp.fr
Date: Thu Feb 23 2006 - 16:59:07 CST

Selon John Stone <johns_at_ks.uiuc.edu>:
Hello,
good remark. No, I don't use the -eofexit flag when I run the VMD command line.
I using something like that:
vmd -psf myfile.psf -dispdev none -e myscript.vmd -args ouputdir mytraj.dcd

Nicolas

>
> 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
>

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