From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Oct 19 2010 - 10:39:50 CDT

Hi,
  Something is fishy with the DCD file produced by Vega ZZ, it is
triggering a type of error handling loop in the VMD DCD plugin repeatedly
trying to do a seek. I will have to debug this carefully and get back to you.

Cheers,
  John

On Tue, Oct 19, 2010 at 04:21:44PM +0200, Ajasja Ljubeti?? 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?
> 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)

-- 
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