From: Ajasja Ljubetič (
Date: Tue Oct 19 2010 - 09:21:44 CDT

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,

Info) VMD for WIN32, version 1.8.7 (August 1, 2009)
Info) Email questions and bug reports to
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) 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)