Re: [Apbs-users] APBS electrostatics in VMD

[Shuangxing D. <shu...@gm...>]

Well, I tried the same simulation on both Mac OS 10.7 and 10.6 and the same problem exists. The memory are 8G and 10G. So I think memory is enough. I also tried the VMD 1.8.7. The same problem also. So maybe I should try the windows version?
Thanks,
Shuangxing Dai

On Jul 26, 2011, at 10:46 AM, John Stone wrote:

> 
> Hi,
>  Thanks for that information.  I'm very surprised to see that this is 
> a Mac, as the MacOS X drivers had been working fine for some time now.  
> I wonder if they recently broke the video driver in an OS update,
> or if this is simply a case where your video card doesn't have enough
> free video memory left by the time VMD goes to render the 3-D texture.
> I see that your GPU only supports small 3-D texture maps to start with,
> so this may be an potential indication.  Did you have any other graphical
> applications running on this machine while using VMD?  Have you tried 
> displaying a smaller 3-D texture map?
> 
> Which version of MacOS X is running on your machine?
> What output do you get from this command:
>  sw_vers
> 
> I see that you're using a beta version of VMD 1.9 rather than the
> final release version.  It's generally best to use the production versions
> of VMD once they are released, as there are sometimes bugs in the beta
> versions.  I don't think this is affecting your volumetric texturing issue,
> but I thought I should mention it.
> 
> Cheers,
>  John Stone
>  vm...@ks...
> 
> On Tue, Jul 26, 2011 at 10:39:01AM -0400, Shuangxing Dai wrote:
>> Hi, 
>> Thanks, here is the information:
>> 
>> eng5-dhcp23:~ shuangxingdai$ /Applications/VMD/VMD\ 1.9.app/Contents/MacOS/startup.command ; exit;
>> Info) VMD for MACOSXX86, version 1.9beta3 (March 7, 2011)
>> Info) http://www.ks.uiuc.edu/Research/vmd/                         
>> Info) Email questions and bug reports to vm...@ks...           
>> 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, 8 CPUs detected.
>> Info) No CUDA accelerator devices available.
>> Info) OpenGL renderer: NVIDIA GeForce GT 120 OpenGL Engine
>> Info)   Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF) 
>> Info)   Full GLSL rendering mode is available.
>> Info)   Textures: 2-D (8192x8192), 3-D (256x256x256), Multitexture (8)
>> Info) Dynamically loaded 2 plugins in directory:
>> Info) '/Applications/VMD/VMD 1.9.app/Contents/vmd/plugins/MACOSXX86/molfile'.
>> vmd > Jul 26 10:31:01 eng5-dhcp23.bu.edu VMD[44172] <Error>: kCGErrorInvalidConnection: CGSGetWindowTags: Invalid connection
>> Jul 26 10:31:01 eng5-dhcp23.bu.edu VMD[44172] <Error>: kCGErrorFailure: Set a breakpoint @ CGErrorBreakpoint() to catch errors as they are logged.
>> 
>> 
>> 
>> On Jul 26, 2011, at 10:36 AM, John Stone wrote:
>> 
>>> Hi,
>>> It looks like your machine has a broken graphics driver.  
>>> Can you send me the VMD OpenGL startup messages that are printed
>>> in the text console when you first run it?
>>> 
>>> Cheers,
>>> John Stone
>>> vm...@ks...
>>> 
>>> On Tue, Jul 26, 2011 at 09:54:55AM -0400, Shuangxing Dai wrote:
>>>> Yes, it is like this:
>>>> 
>>>> 
>>>> As you see, the color is not correct and not complete.
>>>> So is there any solution?
>>>> Thanks,
>>>> Shuangxing Dai
>>>> 
>>>> On Jul 25, 2011, at 10:45 PM, Baker, Nathan wrote:
>>>> 
>>>>> Hello ?
>>>>> 
>>>>> Please send us a picture of the surface you obtain.  This sounds like a graphics card driver issue that is known in VMD.
>>>>> 
>>>>> Thanks,
>>>>> 
>>>>> __________________________________________________ 
>>>>> Nathan Baker
>>>>> Pacific Northwest National Laboratory
>>>>> Tel:  509-375-3997
>>>>> http://kdi.pnl.gov/bios/baker.stm
>>>>> 
>>>>> From: Shuangxing Dai [mailto:shu...@gm...] 
>>>>> Sent: Monday, July 25, 2011 3:32 PM
>>>>> To: apb...@li...
>>>>> Subject: [Apbs-users] APBS electrostatics in VMD
>>>>> 
>>>>> Hi, all:
>>>>> I followed the step by using files and steps in tutorials on APBS website:
>>>>> 
>>>>> http://www.poissonboltzmann.org/apbs/examples/visualization/apbs-electrostatics-in-vmd
>>>>> 
>>>>> But I cannot get the same picture. Only half of the surface is shown and the color is not correct even after I changed the color scale. Anyone got correct result of this tutorial and know what happens? Thanks in advance.
>>>>> Thanks,
>>>>> Shuangxing Dai
>>>>> 
>>>> 
>>> 
>>> -- 
>>> 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