VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Apr 18 2012 - 21:10:24 CDT

On Wed, Apr 18, 2012 at 9:08 PM, Andrew DeYoung <adeyoung_at_andrew.cmu.edu> 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?

it is in whatever units the property is in that you are
visualizing (i.e. strictly speaking a gromacs question).

the internet has many resources that can save you from
embarrassing questions, for example this one:

http://en.wikipedia.org/wiki/Isosurface

cheers,
    axel.

>
>
> Thank you for your time!
>
> Andrew DeYoung
> Carnegie Mellon University
> 

--
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.