VMD-L Mailing List

From: Amir Hajiahmadi Farmahini (afa047_at_uib.no)
Date: Fri May 28 2010 - 05:40:15 CDT

Hi,

I have simple questions regarding RDF and coordination number in VMD.
Due to some problem I got confused by the way VMD calculates RDF and
Coordination number.Unfortunately VMD user guide is not clear in this
case .

1- VMD asks for two selections to compute RDF. Which one is considered
as central atom and which one is being counted around the central atom.
I assumed that the second selection is counted around the first
selection within r(max)distance. Is that correct?

2- In the Out put file third column (igr)is the coordination number and
the fourth(isto) is the unnormalized histogram. Is that true?
I guess the igr is the right number when we need to know the number of
surrounding atom in vicinity of the atom of interest.

Thanks in advance.

Amir