VMD-L Mailing List

From: David Slochower (slochower_at_gmail.com)
Date: Fri Nov 22 2013 - 12:56:35 CST

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