VMD-L Mailing List

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Tue Oct 19 2010 - 11:56:26 CDT

Thank you both.
For now I will just hexedit the DCDs.
I'm on windows and I'm afraid to even ask for win alpha build:)
I will also contact the Vega ZZ authors.

Best regards,
Ajasja

On Tue, Oct 19, 2010 at 18:28, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> 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 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.
>
> --
> 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
>