VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Sep 04 2006 - 22:38:40 CDT

Hi,
  If you're using the "bigdcd" script, you're going to have to change it
so that you wait until the last frame has been loaded, otherwise it'll
run briefly and terminate (as you discovered) before it's really done,
since it works by loading frames in the background. I'll ask Leo to bounce
a copy of his version of this script to the list, since he was doing
the same thing recently..

  John

On Mon, Sep 04, 2006 at 04:31:33PM +0200, Gordon Wells wrote:
> 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 

-- 
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/      Fax: 217-244-6078