VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon May 07 2012 - 16:19:34 CDT

Hi,
  I think the root of your problem is your version 0.4 OpenGL driver:
Info) OpenGL renderer: Gallium 0.4 on NV86

What kind of GPU is actually in your machine?
Is this an NVIDIA GPU running some kind of open source driver?
If so, I would recommend that you get rid of the open source driver
and install the real NVIDIA drivers. The open source drivers are
pretty useless when it comes to running heavy duty OpenGL apps like VMD.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, May 07, 2012 at 03:54:51PM -0500, Wei Chen wrote:
> I am using Quadro NVS 290.
>
> Following is the start up message:
>
> Info) VMD for LINUXAMD64, version 1.9.1 (February 1, 2012)
> 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: 675MB (33%)
> Warning) Detected a mismatch between CUDA runtime and GPU driver
> Warning) Check to make sure that GPU drivers are up to date.
> 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: Gallium 0.4 on NV86
> Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF)
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (4096x4096), 3-D (512x512x512), Multitexture (8)
> Info) Dynamically loaded 2 plugins in directory:
> Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
> Info) File loading in progress, please wait.
> Info) Using plugin pdb for structure file 3BDC.pdb
> Info) Using plugin pdb for coordinates from file 3BDC.pdb
> Info) Determining bond structure from distance search ...
> Info) Eliminating bonds duplicated from existing structure...
> Info) Finished with coordinate file 3BDC.pdb.
> Info) Analyzing structure ...
> Info) Atoms: 1179
> Info) Bonds: 1100
> Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
> Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
> Info) Residues: 237
> Info) Waters: 106
> Warning) Unusual bond between residues: 21 (protein) and 150 (none)
> Warning) Unusual bond between residues: 40 (protein) and 150 (none)
> Warning) Unusual bond between residues: 41 (protein) and 150 (none)
> Warning) Unusual bond between residues: 43 (protein) and 150 (none)
> Warning) Unusual bond between residues: 150 (none) and 157 (waters)
> Warning) Unusual bond between residues: 150 (none) and 162 (waters)
> Info) Segments: 1
> Info) Fragments: 106 Protein: 1 Nucleic: 0
>
>
> Thank you!
>
> Wei Chen
>
>
> On Mon, May 7, 2012 at 3:39 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
> > This sounds like a bug in your graphics driver.  What GPU are
> > you using?  What startup messages are printed by VMD in the
> > text console?
> >
> > Cheers,
> >  John Stone
> >  vmd_at_ks.uiuc.edu
> >
> > On Mon, May 07, 2012 at 03:17:21PM -0500, Wei Chen wrote:
> >> Hi,
> >>
> >> When I draw a structure using 'Bonds' or 'Licorice' and color it by
> >> 'Name', all bonds are shown as blue instead of different colors. This
> >> happens for all versions of vmd I tried (1.9.1, 1.9, 1.8.6). I am
> >> using a PC with Intel(R) Core(TM)2 Duo CPU. The operating system is
> >> openSUSE 12.1 64bit. Any ideas about the problem?
> >>
> >> Thank you!
> >>
> >> Wei Chen
> >
> > --
> > NIH Resource for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
> > http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078