VMD-L Mailing List

From: Gordon Wells (gordon.wells_at_gmail.com)
Date: Mon Sep 04 2006 - 09:31:33 CDT

Hi Neela

I'm currently using a very small (5 frames) dcd file to test with. The reason
I'm using bigdcd.tcl (from the vmd scripts web page) is to load, analyse and
delete one frame at a time - so hopefully dcd size isn't the problem.

regards
Gordon

On Monday 04 September 2006 16:02, you wrote:
> 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

Gordon Wells
Bioinformatics and Computational Biology Unit
Department of Biochemistry
University of Pretoria