VMD-L Mailing List

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
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,
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)