From: Axel Kohlmeyer (
Date: Tue Dec 22 2009 - 09:08:20 CST

On Tue, 2009-12-22 at 19:47 +0530, gurunath katagi wrote:
> 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.

updating the selections is a waste of time, since the atoms
within the selections don't change.

> But in the plot of g(r) v/s r , the g(r) has reached zero after some
> value of radius.

that is to be expected considering your selection.

> Typically in a RDF curve , the value of g(r) drops down, but is not
> zero ...

those typical g(r)s are for bulk systems.

> I checked this with different atomselections in sel1 and sel2 , I am
> getting the same kind of graph .

you should.

> 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.

the fault is in your head. think about what a radial pair distribution
is computed from and what you use as input here (effectively two
"clusters" not bulk systems) and factor in that the g(r) code applies
minimum image conventions, _iff_ box dimensions are available.


> I have attached one of the graph in .ps format
> Thank you
> Gurunath

Dr. Axel Kohlmeyer 
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.