VMD-L Mailing List

From: Gordon Wells (gordon.wells_at_gmail.com)
Date: Mon Aug 20 2007 - 04:49:51 CDT

I had similar problems. I could the script to run to completion by using my
own "trace variable" but this did not work for queue submissions.

See the following thread, which includes a modified bigdcd.tcl for correct
termination.

http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/7714.html

Hope it helps

On Wednesday 15 August 2007 11:09:32 maria goranovic wrote:
> Hello,
>
> I had posted this earlier on the NAMD list, and was suggested to take it to
> the correct (vmd) forum.
>
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/6392.html
>
> I have a peculiar problem while working with bigdcd.tcl which I downloaded
> off the website, and stored in the directory ~/NAMD_SCRIPTS. Here is the
> problem:
>
> The number of frames that is accessed by my procedure using bigdcd is the
> same as the number of new line characters that appear after the last line
> in the tcl script below. Why would this happen ? THE PROBLEM ONLY APPEARS
> IF I USE VMD ON THE COMMAND LINE. The script runs fine interactively inside
> a vmd console.
>
> Here is the script with 2 example inputs and corresponding outputs. Please
> note that the 2 input scripts only differ in the number of empty lines
> after the last line of the script.
>
> INPUT1:
> #########################3
> source ~/NAMD_SCRIPTS/bigdcd.tcl
> mol load pdb waterprotcharmm.pdb
> proc displacement {frame} {
> puts $frame
> }
>
> bigdcd displacement waterprot-10k.dcd
> #########################3
>
> OUTPUT1:
>
> #########################3
> Info) VMD for LINUX, version 1.8.5 (August 25, 2006)
> Info) http://www.ks.uiuc.edu/Research/vmd/
> Info) Email questions and bug reports to
> vmd_at_ks.uiuc.edu<vmd_at_ks.uiuc.edu?Subject=Re:%20Very%20peculiar%20probl
>em%20while%20using%20bigdcd.%20Help%20%21> Info) Please include this
> reference in published work using VMD:
> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Multithreading available, 2 CPUs detected.
> after#0
> psfplugin) Detected a Charmm31 PSF file
> Info) Using plugin psf for structure file waterprotcharmm.psf
> Info) Analyzing structure ...
> Info) Atoms: 65594
> Info) Bonds: 65802
> Info) Residues: 17818
> Info) Waters: 16810
> Info) Segments: 9
> Info) Fragments: 16818 Protein: 4 Nucleic: 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 waterprot-10k.dcd
> 1
> Info) VMD for LINUX, version 1.8.5 (August 25, 2006)
> Info) Exiting normally
>
> INPUT2:
> #########################
> source ~/NAMD_SCRIPTS/bigdcd.tcl
> mol load pdb waterprotcharmm.pdb
> proc displacement {frame} {
> puts $frame
> }
>
> bigdcd displacement waterprot-10k.dcd
>
>
>
>
> #########################
> OUTPUT2: (same as output 1, except that more frames are accessed
> #########################
> ...
> ...
> 1
> 2
> 3
> 4
> Info) VMD for LINUX, version 1.8.5 (August 25, 2006)
> Info) Exiting normally
> #########################
>
>
> Maria G.
> Technical University of Denmark
> Copenhagen 

-- 
Today is Boomtime, the 13rd day of Bureaucracy in the YOLD 3173
'What is this thing, anyway?' said the Dean, inspecting the implement in 
his hands.'It's called a shovel', said the Senior Wrangler. 'I've seen 
the gardeners use them. You stick the sharp end in the ground. Then it 
gets a bit technical.'
	-- Terry Pratchett, Reaper Man
Gordon Wells
Bioinformatics and Computational Biology Unit
Department of Biochemistry
University of Pretoria