VMD-L Mailing List

From: TAE BUM LEE (taebumlee_at_gmail.com)
Date: Wed Dec 09 2009 - 16:37:42 CST

Hi,

I am doing tutorial from NAMD-tutorial pdf file. For rmsd analysis after MD
simulation of ubiquitin protein, I try to do call psf and dcd followed by
source rmsd.tcl in Tk console. The VMD windows are collapsed abruptly with
segmentation fault error message.
The generated rmsd.dat doesn't have any data in it.

My computer system is Ubuntu 9.10. However, the same situation happen in my
macbook (Intel mac with OSX 10.5).
Does anybody know the solution for this error?

FYI, I attach the terminal message as a scrapbook below.

Thanks,
TaeBum

taebum_at_Aubie:~/Documents/NAMD-tutorial$ ls
1-1-build 2-1-rmsd 2-4-temp 2-7-echoes common
1-2-sphere 2-2-maxwell 2-5-spec-heat 3-1-pullcv README
1-3-box 2-3-energies 2-6-heat-diff 3-2-pullcf
taebum_at_Aubie:~/Documents/NAMD-tutorial$ cd 1-2-sphere/
taebum_at_Aubie:~/Documents/NAMD-tutorial/1-2-sphere$ ls
example-output ubq_ws_eq.dcd ubq_ws_eq.restart.vel.old
rmsd.dat ubq_ws_eq.log ubq_ws_eq.restart.xsc
rmsd.tcl ubq_ws_eq.restart.coor ubq_ws_eq.restart.xsc.old
ubq_ws_eq.conf ubq_ws_eq.restart.coor.old ubq_ws_eq.vel
ubq_ws_eq.coor ubq_ws_eq.restart.vel ubq_ws_eq.xsc
taebum_at_Aubie:~/Documents/NAMD-tutorial/1-2-sphere$ vmd
Info) VMD for LINUX, 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, 2 CPUs detected.
Info) Free system memory: 635MB (63%)
Info) No CUDA accelerator devices available.
Warning) Detected X11 'Composite' extension: if incorrect display occurs
Warning) try disabling this optional X server feature.
Info) OpenGL renderer: GeForce FX 5700/AGP/SSE2
Info) Features: STENCIL MSAA(4) MDE CVA MTX PP PS GLSL(OVF)
Warning) GPU driver failed to compile shader:
Warning) /usr/local/lib/vmd/shaders/vmd
Warning) This GPU/driver is buggy, or doesn't fully implement GLSL.
Warning) Set environment variable VMDGLSLVERBOSE for more info.
Info) GLSL rendering mode is NOT available.
Info) Textures: 2-D (4096x4096), 3-D (512x512x512), Multitexture (4)
vmd > psfplugin) Detected a Charmm31 PSF file
Info) Using plugin psf for structure file
/home/taebum/Documents/NAMD-tutorial/common/ubq_ws.psf
Info) Analyzing structure ...
Info) Atoms: 6682
Info) Bonds: 4871
Info) Angles: 4074 Dihedrals: 3293 Impropers: 204 Cross-terms: 74
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 1893
Info) Waters: 1817
Info) Segments: 2
Info) Fragments: 1818 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)
Info) Using plugin dcd for coordinates from file
/home/taebum/Documents/NAMD-tutorial/1-2-sphere/ubq_ws_eq.dcd
Info) Finished with coordinate file
/home/taebum/Documents/NAMD-tutorial/1-2-sphere/ubq_ws_eq.dcd.
Segmentation fault
taebum_at_Aubie:~/Documents/NAMD-tutorial/1-2-sphere$ cat rmsd.dat
taebum_at_Aubie:~/Documents/NAMD-tutorial/1-2-sphere$

########################################
TAE BUM LEE
Dept. Chem. & Biochem
Auburn Univ. AL. 36849
TEL.: 334-844-6912
e-mail: taebumlee_at_gmail.com
########################################