VMD-L Mailing List

From: zhenlong li (zxl1000_at_gmail.com)
Date: Fri May 09 2008 - 08:34:41 CDT

John,

 For the original version, I ran it before as you told me here and only got

the result of first frame. But I found out the modified version of
bigdcd.tcl, and called

the bigdcd to wait at the end of my script. It works well. Aslo, Axel has
posted an

improved version of bigdcd, I think it is a final solution to this problem.

Thank you both!

with best wishes

Zhenlong

On Fri, May 9, 2008 at 3:29 AM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> 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/ <http://www.ks.uiuc.edu/%7Ejohns/>
> Fax: 217-244-6078
> 

-- 
Zhenlong