VMD-L Mailing List

From: Gordon Wells (gordon.wells_at_gmail.com)
Date: Mon Sep 04 2006 - 08:25:54 CDT

Hi

I'm trying to run a frame by frame rmsd-per-residue analysis using a
combination of code from the bigdcd.tcl and residue_rmsd.tcl scripts.
The analysis runs fine manually, but vmd dies prematurely when launched from
my qsub script. The exit corresponds to when the command prompt returns
(after the third frame) in vmd. Is it possible to let vmd run scripts to
completion with qsub?

Here is the qsub script:
#!/bin/bash
#
#PBS -N rmsd-per-res-noMg-chB
#PBS -l nodes=1
#PBS -q md

dir=~/nd-solv-fug-sym-nomg
cd $dir

echo "group main" > rmsdhost

counter=0
for node in `cat $PBS_NODEFILE`; do
    echo "host $node" >> rmsdhost;
done;

ssh $node "cd $dir; vmd-1.8.5 -dispdev text -e rmsd-per-res.tcl >
rmsd-per-resChB.out"

The tcl:

mol new equilall-somemore.coor
mol addfile ionized.psf molid 0
source bigdcd.tcl
pre_rmsd_per_res 0 "segid ARB1 or segid ARB2" test.dat test.res 0
set finished 0
trace variable vmd_frame w rmsd_per_res_callback
bigdcd rmsd_per_res small.dcd

The trace is meant to do the final calculations, and quit vmd, but is never
reached when running from qsub.

Lastly, the vmd output:

# tail -f rmsd-per-resChB.out
Info) Waters: 26855
Info) Segments: 15
Info) Fragments: 26886 Protein: 6 Nucleic: 0
0
0
dcdplugin) detected standard 32-bit DCD file of native endianness
dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
Info) Using plugin dcd for coordinates from file small.dcd
1: 1.06965327263
2: 1.08540391922
3: 1.07799816132
Info) VMD for LINUX, version 1.8.5 (August 25, 2006)
Info) Exiting normally.

Thanks in advance
gordon 

-- 
POLITICS, n.  A strife of interests masquerading as a contest of
principles.  The conduct of public affairs for private advantage.
  -- Ambrose Bierce, The Devil's Dictionary
Gordon Wells
Bioinformatics and Computational Biology Unit
Department of Biochemistry
University of Pretoria