From: Axel Kohlmeyer (
Date: Wed Mar 05 2008 - 12:45:36 CST

On Wed, 5 Mar 2008, Giovanni Bellesia wrote:

GB> Hi,
GB> a quick question on the g(r) GUI plugin. I'm using it to calculate how the
GB> presence of a small peptide perturbates
GB> the water structure in its vicinity. I'm skipping the details of the
GB> calculation here but I'm using the selection
GB> "water and same residue as within XX from protein" with several values of XX

hmmm... it is difficult to give a recommendation if you don't specify
what you are looking for and what exactly you enter for _both_
selections. e.g. if you enter the selection text from above for both
entries you get something completely meaningless as you'll get the
rdf from everything to everything. already using "water" is bad, as
it includes the oxygens _and_ the hydrogens.

GB> just to see how the perturbation decays.

actually, if you are just interested into the the relative structure
away from the protein, you don't need multiple selections. just pick
a large value of XX and be happy.

however, if you - as i suspect - want the relative structure changes
orthogonal to the surface of the protein, you cannot use the gofr code
at all, as it is computing a 3d isotrope distribution function.

GB> Now, I'm reading on the VMD website:
GB> "Note, that the normalization of g(r) has little meaning unless you enable
GB> processing of the periodic boundary condition
GB> and have a fixed set of atoms in the selection.
GB> The number integrals are computed directly and thus provide accurate
GB> coordination numbers."

GB> Since I'm interested in the number integrals, I'd like to know if
GB> the last line actually means that the number integrals are correct
GB> even if the number of atoms varies from one frame to another

yes. it is computed from directly summing up the histrograms before
normalization. the most important step to get meaningful results is
to be very careful in the formulation of the selection texts.
the plugin cannot really help you there...


GB> Thanks
GB> Giovanni

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.