VMD-L Mailing List

From: Himanshu Khandelia (hkhandel_at_memphys.sdu.dk)
Date: Mon May 07 2007 - 10:25:56 CDT

Hi Axel,

Thank you for the tip. Using the -e option allows bigdcd to read all the
frames. However, I had problems when I tried to add "after idle { quit }"
to the end of my script.

Adding "after idle { quit }" results in a syntax error. Also the number of
frames accessed in my script (posted earlier) is dependent upon the number of
blank lines between the end of my script and "after idle { quit }.

For example if I have 0 blank lines between the last line of my script and
the line "after idle { quit }", I get the following:
######################################
this is frame number 1
this is frame number 2
after#1
Info) VMD for LINUX, version 1.8.5 (August 25, 2006)
Info) Exiting normally.
    while executing
"quit "
    ("after" script)
######################################

If, on the other hand, I have 1 blank lines between the last line of my
script and the line "after idle { quit }", I get the following:

######################################
this is frame number 1
this is frame number 2
this is frame number 3
after#1
Info) VMD for LINUX, version 1.8.5 (August 25, 2006)
Info) Exiting normally.
    while executing
"quit "
    ("after" script)
######################################

... and so on.

Any idea why this is happening ?

Thank you !

-Himanshu

On Mon, 7 May 2007, Axel Kohlmeyer wrote:

> On Mon, 7 May 2007, Himanshu Khandelia wrote:
>
> HK> Hi,
> HK>
> HK> I am trying to use bigdcd.tcl, but vmd stops after reading one frame with
> HK> no errors. My trajectory does have multiple frames, and was obtained by
> HK> merging using catdcd. I cannot figure out what is wrong.
> HK>
> HK> I am implementing the above script using
> HK>
> HK> vmd -dispdev text < myscript.tcl
>
> please try running:
>
> vmd -dispdev text -e myscript.tcl
>
> and then wait until you see 'bigdcd done' before typing 'quit'
> or put 'after idle { quit }' at the end of your script.
>
> to explain: bigdcd loads the trajectory in background
> so you have to wait until bigdcd is done, before you
> can quite the tcl interpreter.
>
> cheers,
> axel.
>
> HK>
> HK> Here is the exact output:
> HK>
> HK> ####################################
> HK> Info) VMD for LINUX, version 1.8.5 (August 25, 2006)
> HK> Info) http://www.ks.uiuc.edu/Research/vmd/
> HK> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> HK> Info) Please include this reference in published work using VMD:
> HK> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> HK> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> HK> Info) -------------------------------------------------------------
> HK> Info) Multithreading available, 2 CPUs detected.
> HK> psfplugin) Detected a Charmm31 PSF file
> HK> Info) Using plugin psf for structure file proteincharmm.psf
> HK> Info) Analyzing structure ...
> HK> Info) Atoms: 15228
> HK> Info) Bonds: 15436
> HK> Info) Residues: 1008
> HK> Info) Waters: 0
> HK> Info) Segments: 5
> HK> Info) Fragments: 8 Protein: 4 Nucleic: 0
> HK> 0
> HK> Info) Using plugin pdb for coordinates from file protein.pdb
> HK> Info) Finished with coordinate file protein.pdb.
> HK> dcdplugin) detected standard 32-bit DCD file of native endianness
> HK> dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
> HK> Info) Using plugin dcd for coordinates from file protein.dcd
> HK> this is frame number 1
> HK> Info) VMD for LINUX, version 1.8.5 (August 25, 2006)
> HK> Info) Exiting normally.
> HK> ####################################
> HK>
> HK> Thanks very much !
> HK>
> HK> -Himanshu
> HK>
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
>
>