From: Axel Kohlmeyer (
Date: Mon Apr 07 2008 - 16:01:54 CDT

On Mon, 7 Apr 2008, Raul Araya wrote:

RA> Thanks Axel for your answer.

RA> My system is periodic but not homogeneous, it is a water channel surrounded
RA> by lipids and water and I want to
RA> calculate the RDF of the waters (O-O and O-H) inside the channel and also
RA> the RDF (O-O and O-H) between

the plugin only computes 3d g(r)s.
in your case this is of limited use. you should compute 2-d g(r)s,
either per slice in z-direction or averaged over them. or even
radial density distributions around the center of your channel.

RA> some main chain carbonyl oxigens from the channel and waters inside the
RA> pore. My problem is that some times I have triyed to do this I got values of
RA> G(r) > 100 for example (when I select the waters between some value in the Z
RA> axis that correspond to the channel axis) but if I select all waters the
RA> values of G(r) are < 1.
RA> what do you think about that?

the normalization is always computed for the whole cell.
the plugin has no knowlege of how you partition your system
with a selection. and unless your selection is solely based
on volume, there is no way to determine a proper normalization.

if you have little water in total, your relative density
(and that is what a g(r) is) will be high. if you turn this
around it will be low.

RA> In all cases I select the "update selection" option and the PBC conditions
RA> acording to the size of mi cell.

you may actually get more consistent numbers with PBC turned off.
but in any case, you'll probably have to write an analysis
script that takes the specifics of your geometry into account.
a generic tool cannot do this. :-(


RA> Any help will be nice... thanks.
RA> Raul

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.