VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Dec 10 2009 - 10:28:16 CST

Hi,
  How large is the DCD file that you're attempting to load?
I'm wondering if you are running out of memory when you load
the DCD file. Another thought I had is that it's conceivable your
DCD file is corrupted in some way, but I wouldn't expect the behavior
you're seeing. How much memory does your other machine have?
Do you have either machine set for a non-US locale (internationalization)?

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Dec 09, 2009 at 04:37:42PM -0600, TAE BUM LEE wrote:
> 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
> ######################################## 

-- 
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