VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Fri Mar 01 2013 - 09:49:31 CST

The x-axis of the g(r) plots is in angstroms, not nanometers. The plot
is exactly correct, it just is not always helpful. For instance, a
selection of "protein" and "lipid" will calculate more interatomic
contacts than you probably intend, as it will give you the distribution
of distance between every atom of your protein and every atom of lipid
in the system, which usually is not very informative when trying to
analyze structure.
Hope this helps!
-Josh Vermaas

On 03/01/2013 03:05 AM, Bharath K. Srikanth wrote:
> Hi all,
>
> I'm trying to calculate the radial pair distribution function of a protein
> with respect to a lipid bilayer. Could you please inform me whether the
> values on the x-axis (of the graph obtained from the vmd script gofr) are
> absolute distance (in nm), or some other form of normalized distance? If
> it is absolute distance, I need to try again, because my graph's values
> are incorrect.
>
> Sincerely
>