VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Dec 11 2009 - 16:12:22 CST

Hi,
  Interesting. I suspect that the locale may be giving you problems
for some reason, though I'm not sure why it would have any effect on
the DCD reader plugin. Can you do me a favor and run VMD like this
on your linux machine: vmd -debug
That will start up gdb and from there you should be able to type "run"
and then go through the same steps that caused you trouble previously.
Once you get to the point where the crash occurs, type the command "where"
into gdb, and email me the results you get. If I can figure out what's
going on there, I might be able to give you a new plugin that fixes your
problem.

Another temporary solution for you to try is to change your
internationalization settings to English or the "C" locale, and see
if the problem goes away or not.

Regarding background/batch processing, yes, in fact you can run VMD
without any graphics/GUI shell in a text-only mode, and even in a
non-interactive batch type mode. This is described in the VMD User's
guide. Let me know if you have more questions about that.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Dec 10, 2009 at 05:42:04PM -0600, TAE BUM LEE wrote:
> Hi,
> The size of DCD is 784K. Physical memory is 1GB while swap memory is 3GB.
> My machine has a support for Korean language and my desktop setting is for
> Korean.
> Isn't there anyway to do rmsd.tcl in background mode(command mode)? It is
> not necessary to me to do in GUI mode for RMSD.dat file.
> Regards,
> TaeBum
>
> 2009/12/10 John Stone <johns_at_ks.uiuc.edu>
>
> 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
>
> --
> ########################################
> 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