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