VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Oct 19 2010 - 11:02:34 CDT

On Tue, Oct 19, 2010 at 10:21 AM, Ajasja Ljubetič
<ajasja.ljubetic_at_gmail.com> wrote:
> Dear All,
> I wanted to perform a conformational search 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, although in this test trajectory there are
> only 6 frames. I have tried manually setting 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.