VMD-L Mailing List
From: David Slochower (slochower_at_gmail.com)
Date: Fri Nov 22 2013 - 17:46:21 CST
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Hi John and all,
Here is a .tar.gz file that has the two cube files -- electron density and
electrostatic potential -- along with a VMD saved state that shows (a) the
isodensity surface stays gray when I set it to color by volume using the
potential yet (b) creating a volume slice using the potential does use the
color range.
https://sites.google.com/site/slochower/home/vmd-isodensity-potential.tar.gz
Thanks,
Dave
On Fri, Nov 22, 2013 at 2:19 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
> 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/
>
- Next message: John Stone: "Re: H-atoms placed at the end in PDB file"
- Previous message: Juan R. Perilla: "Re: Problems with large solvation boxes"
- In reply to: John Stone: "Re: Mapping Gaussian electrostatic potential to electron density with cube files"
- Next in thread: Clark II, Jeffrey Keith: "Re: Mapping Gaussian electrostatic potential to electron density with cube files"
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