From: gurunath katagi (
Date: Tue Dec 22 2009 - 08:17:57 CST

Dear all,
I have calculated the radial distribution function between two groups in
protein using the GofrGui plugin /measure gofr function for simulation
trajectory done using NAMD on a protein using the following procedure .

set sel1 [atomselect top "segname F"]
set sel2 [atomselect top "chain B and resid 93"]
measure gofr $sel1 $sel2 delta 0.1 rmax 20 first 0 last 24 step 1
I have also used pbc and update selection.

But in the plot of g(r) v/s r , the g(r) has reached zero after some value
of radius.
Typically in a RDF curve , the value of g(r) drops down, but is not zero ...
I checked this with different atomselections in sel1 and sel2 , I am getting
the same kind of graph .

Can anybody kindly help me figure out the mistake, like what does it
indicate ? -- any faults in the simulation part or any atomselection or
something else.
I have attached one of the graph in .ps format

Thank you