VMD-L Mailing List

From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Mon Sep 04 2006 - 09:02:16 CDT

Hi Gordon,

Is your dcd file very large? I have faced a similar issue with VMD quitting
prematurely, when my dcd was too large. Your memory has to be large enough
to hold your entire dcd trajectory. My solution was to take parts of the
trajectory and run my script, and later concatenate my output files.

Best,
 Neela

On 9/4/06, Gordon Wells <gordon.wells_at_gmail.com> wrote:
>
> 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
>
>