VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Apr 18 2012 - 20:49:08 CDT

Hi,
  The units are whatever the units of the data you loaded were.
The values in the isovalue slider correspond directly to the data
values that the associated VMD molfile plugin read from the input file,
unless some kind of unit conversion was done on the fly, but in the case
of volumetric data, none of the existing plugins do any unit conversions...
The reason the units aren't specified is that many of the existing
volumetric file formats don't include any provision to label the units
in the file, and/or the programs that generate the volumetric files don't
bother to write the units even if the file format supports it.
The units of the isovalue slider in VMD are therefore directly related
to the per-voxel scalar values stored in the volumetric data file,
e.g. a density value (not the cartesian coordinates, not lengths, etc).

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Apr 18, 2012 at 09:08:53PM -0400, Andrew DeYoung wrote:
> Greetings,
>
> I am a little embarrassed to be asking this, but somehow I cannot seem to
> find the answer. The Isovalue Drawing Method in VMD draws surfaces based on
> a volumetric data set. For example, I have used the Gromacs utility
> g_spatial (http://www.gromacs.org/Documentation/Gromacs_Utilities/g_spatial)
> to compute the spatial distribution function of a set of molecules around
> reference atom(s). The utility outputs the results in Gaussian 98 cube
> format. I load the file into VMD and select the Isovalue Drawing Method. A
> few controls appear, including an Isovalue slider.
>
> My question is, what are the units of the Isovalue slider? Is it a length
> (for example, the radius of a sphere in which to consider molecules around
> the reference)? Or is it a density (for example, a number density in units
> of atoms/Angstrom^3 or atoms/nm^3)? Or, is this more of a Gromacs question
> than a VMD question?
>
> Thank you for your time!
>
> Andrew DeYoung
> Carnegie Mellon University 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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