VMD-L Mailing List

From: Andrew DeYoung (adeyoung_at_andrew.cmu.edu)
Date: Wed Apr 18 2012 - 20:52:13 CDT

Dr. Stone,

Thanks for your help. I will try to look deeper in the Gromacs code.

Andrew

-----Original Message-----
From: John Stone [mailto:johns_at_ks.uiuc.edu]
Sent: Wednesday, April 18, 2012 9:49 PM
To: Andrew DeYoung
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: Units of Isovalue Slider in Isovalue Drawing Method

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
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