VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Nov 22 2013 - 13:19:10 CST

Hi,
  Can you provide a URL link to a tar.gz or .zip file the input files
and the VMD saved state that will reproduce the problem? I will need
to inspect both your input files and the saved state to give you a suggestion.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Nov 22, 2013 at 01:56:35PM -0500, David Slochower wrote:
> Hi all.
> I've encountered unexpected behavior trying to map an electrostatic
> potential (from a Gaussian 09 revision A.02 cube file) onto an electron
> density surface (also a Gaussian cube file). Both files load in without
> any error:
> Info) Analyzing Volume...
> Info) Grid size: 92x80x70 (7 MB)
> Info) Total voxels: 515200
> Info) Min: -0.320400 Max: 83.804398 Range: 84.124794
> Info) Computing volume gradient map for smooth shading
> I can visualize the electron density in VMD 1.9.1 as an isosurface, but
> when I try to color by volume using the potential cube file, the surface
> color never changes for any color scale data range under the trajectory
> tab (http://i.imgur.com/i5b8TrS.png). The net charge of the molecule is -2
> and all the values in the potential cube file are negative, but I don't
> think this should be a problem.
> Drawing a separate VolumeSlice with the potential does give proper
> coloring (http://i.imgur.com/pcIMmR7.png). For what it's worth, GaussView
> 5.0.8 in Windows can correctly map the potential to the electron density.
> CUDA and OpenGL seem to be working properly:
> Info) Multithreading available, 8 CPUs detected.
> Info) Free system memory: 6225MB (51%)
> Info) Creating CUDA device pool and initializing hardware...
> Info) Detected 1 available CUDA accelerator:
> Info) [0] GeForce GTX 275 30 SM_1.3 @ 1.46 GHz, 895MB RAM, KTO, OIO,
> ZCP
> [...]
> Info) OpenGL renderer: GeForce GTX 275/PCIe/SSE2
> Info) Features: STENCIL MSAA(16) MDE CVA MTX NPOT PP PS GLSL(OVFG)
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (8192x8192), 3-D (2048x2048x2048), Multitexture (4)
> Any suggestions are welcome.
> Thanks,
> Dave 

-- 
NIH Center 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/