From: Wei Chen (cwbluesky_at_gmail.com)
Date: Mon May 07 2012 - 16:44:19 CDT

Hi John,

You are right. Previously, I was using the open source nouveau driver.
After I installed Nvidia driver, things are working great!

Thanks a lot!

Wei

On Mon, May 7, 2012 at 4:19 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> 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