From: Andrew DeYoung (
Date: Wed Apr 18 2012 - 20:08:53 CDT


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 (
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