From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Oct 19 2010 - 11:28:45 CDT

Hi,
  Axel is exactly right, and this agrees with what I saw running the code.
This file is just badly formatted, and Vega ZZ needs to be fixed to write
DCD files correctly.

I have changed the VMD DCD plugin to detect bogus values for NTITLE, and
it will even check for the specific bogus value that your file contained
and detect it as an incorrectly formatted DCD file produced Vega ZZ, and
can workaround the problem. I don't know if the workaround will work for
any other DCD file produced by Vega ZZ, but it will work for yours.

At the very least, anyone else trying to load a badly formatted Vega ZZ file
will not get the "hanging" type behavior you experienced where the DCD plugin
was blindly trusting that the huge NTITLE value was correct and was
dutifully trying to skip past 1095062083 lines of text. :-)
The new code will emit warnings and will drop out of the NTITLE code
if it finds ridiculous values larger than 1000 or less than zero.

I will have a Linux alpha build of VMD available that includes this update
by tomorrow if you want to try it.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Oct 19, 2010 at 12:02:34PM -0400, Axel Kohlmeyer wrote:
> On Tue, Oct 19, 2010 at 10:21 AM, Ajasja Ljubeti??
> <ajasja.ljubetic_at_gmail.com> wrote:
> > Dear All,
> > I wanted to perform aconformationalsearch on a spin label.The simplest
> > way seemed to me, to use Vega ZZ to generate a trajectory of different
> > rotamers and analyze the results using VMD/NAMD. But if I try to open the
> > trajectory file then VMD stops responding. The CPU goes to max (for one
> > thread) and nothing much happens,althoughin this test trajectory there are
> > only 6 frames. I have triedmanuallysetting first and last frame but that
> > didn't help. Any suggestions?
>
> the dcd file that you have is broken. a quick check with a debugger and
> a hex editor shows that Vega ZZ seems to be writing the dcd header wrong.
> there needs to be an integer telling how many title strings of 80 char length
> are in the header. instead the title strings start immediately triggering VMD
> to search for an insane amount of these strings (1095062083 to be exact).
>
> if i overwrite those characters with the proper bytes signifying two 80char
> strings in a hex editor, the read proceeds normally. i would suggest contacting
> the vega zz author(s) about this issue. to correct manually, you could use
> the hexl mode in (x)emacs as shown below.
>
> hex editor before:
> 00000000: 5400 0000 434f 5244 0000 0000 0000 0000 T...CORD........
> 00000010: 0000 0000 0000 0000 0000 0000 0000 0000 ................
> 00000020: 0000 0000 0000 0000 0000 0000 0000 0000 ................
> 00000030: 0000 0000 0000 0000 0000 0000 0000 0000 ................
> 00000040: 0000 0000 0000 0000 0000 0000 0000 0000 ................
> 00000050: 0000 0000 1800 0000 5400 0000 5400 0000 ........T...T...
> 00000060: 4352 4541 5445 4420 4259 2056 4547 4120 CREATED BY VEGA
> 00000070: 5a5a 2032 2e34 2e30 2020 2020 2020 2020 ZZ 2.4.0
> 00000080: 2020 2020 2020 2020 2020 2020 2020 2020
> 00000090: 2020 2020 2020 2020 2020 2020 2020 2020
> 000000a0: 2020 2020 2020 2020 2020 2020 2020 2020
> 000000b0: 2020 2020 2020 2020 2020 2020 2020 2020
> 000000c0: 2020 2020 2020 2020 2020 2020 2020 2020
> 000000d0: 2020 2020 2020 2020 2020 2020 2020 2020
> 000000e0: 2020 2020 2020 2020 2020 2020 2020 2020
> 000000f0: 2020 2020 2020 2020 2020 2020 2020 2020
> 00000100: 2020 2020 a400 0000 0400 0000 2800 0000 ........(...
>
> hex editor after:
> 00000000: 5400 0000 434f 5244 0000 0000 0000 0000 T...CORD........
> 00000010: 0000 0000 0000 0000 0000 0000 0000 0000 ................
> 00000020: 0000 0000 0000 0000 0000 0000 0000 0000 ................
> 00000030: 0000 0000 0000 0000 0000 0000 0000 0000 ................
> 00000040: 0000 0000 0000 0000 0000 0000 0000 0000 ................
> 00000050: 0000 0000 1800 0000 5400 0000 5400 0000 ........T...T...
> 00000060: 0200 0000 5445 4420 4259 2056 4547 4120 ....TED BY VEGA
> 00000070: 5a5a 2032 2e34 2e30 2020 2020 2020 2020 ZZ 2.4.0
> 00000080: 2020 2020 2020 2020 2020 2020 2020 2020
> 00000090: 2020 2020 2020 2020 2020 2020 2020 2020
> 000000a0: 2020 2020 2020 2020 2020 2020 2020 2020
> 000000b0: 2020 2020 2020 2020 2020 2020 2020 2020
> 000000c0: 2020 2020 2020 2020 2020 2020 2020 2020
> 000000d0: 2020 2020 2020 2020 2020 2020 2020 2020
> 000000e0: 2020 2020 2020 2020 2020 2020 2020 2020
> 000000f0: 2020 2020 2020 2020 2020 2020 2020 2020
> 00000100: 2020 2020 a400 0000 0400 0000 2800 0000 ........(...
>
> [akohlmey_at_fermi Downloads]$ ./dcdplug-debug.x CMTS_VAC.relaxed.dcd
> dcdplugin) detected standard 32-bit DCD file of native endianness
> dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
> main) file: CMTS_VAC.relaxed.dcd
> 40 atoms, 6 frames, size: 0.0MB
> Time: 0.0 seconds
> Speed: 151.6 MB/sec, 331129.3 timesteps/sec
> Overall Size: 0.0 MB
> Overall Time: 0.0 seconds
> Overall Speed: 151.6 MB/sec
>
> cheers,
> axel.
>
> > Best regards,
> > Ajasja
> > Info) VMD for WIN32, version 1.8.7 (August 1, 2009)
> > Info) http://www.ks.uiuc.edu/Research/vmd/
> > Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> > 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, 4 CPUs detected.
> > Info) Free system memory: 4095MB (100%)
> > Info) Detected 1 available CUDA accelerator:
> > Info) [0] GeForce GTS 250 16 SM_1.1 @ 1.85 GHz, 1005MB RAM, OIO
> > Info) Creating CUDA device pool and initializing hardware...
> > Info) OpenGL renderer: GeForce GTS 250/PCI/SSE2
> > Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF)
> > Info) Full GLSL rendering mode is available.
> > Info) Textures: 2-D (8192x8192), 3-D (2048x2048x2048), Multitexture (4)
> > Info) No joysticks found. Joystick interface disabled.
> > Info) Using plugin psf for ***
> > psfplugin) no cross-terms defined in PSF file.
> > Info) Analyzing structure ...
> > Info) Atoms: 40
> > Info) Bonds: 40
> > Info) Angles: 74 Dihedrals: 101 Impropers: 12 Cross-terms: 0
> > Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
> > Info) Residues: 1
> > Info) Waters: 0
> > Info) Segments: 1
> > Info) Fragments: 1 Protein: 1 Nucleic: 0
> > dcdplugin) detected standard 32-bit DCD file of native endianness
> > dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> http://sites.google.com/site/akohlmey/
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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