VMD-L Mailing List

From: zhenlong li (zxl1000_at_gmail.com)
Date: Tue May 06 2008 - 14:40:44 CDT

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