Subject: a question about g(r) for heteroatoms

From: "weiz" <weiz=at=mail.rochester.edu>
Date: Wed, 22 Oct 2003 17:59:17 -0400

Dear Sir:
I have a problem to calculate the g(r) for heteroatoms. the system that I
am studying is a peptide in DMSO system.now I want to calculate the g(r)
for the polar H of peptide (which are
the ones connected to nitrogens) and the peptide Oxygen atoms ( on the C=O
bond),I want to use it to check the intramolecular hydrogen bonding
property of this peptide in different
stages of the peptide dynamics.

ok,now,what I did is based on the algorithm in frenkel's book for the
homoatoms: for one specific stage during the relaxation,I sampled 4000
configurations,then I calcualte all the O-H distances and seperate them
into different bins according to 
the lengths. when a distance falls into one specific bin [r,r+1],I add 1
to the counter GNUM ( in frenkel,it counts 2,but mine is a heteroatom
system,which means I look at the hydrogen \
bonding from the oxygen side), now I calculate the condition for ideal
gas, first I calculate the volume of the bin V,which is 4/3 *
((r+1)^3-r^3),then I need to calculate the number of 
hydrogen atoms fall into this neighbor of one oxygen in the ideal gas
condition,thus I simply use the number density of hydrogen atoms rho(H)
(number of polar H divided by the cell volume )
multiply the bin volume V and the number 4000,GNUM_ig=rho(H)*V*4000,then I
obtain g(r) by GNUM/GNUM_ig.

this method looks ok,but wait!!,if I take a look at the hydrogen bonding
> from hydrogen atoms' side,then GNUM is the same but GNUM_ig will be
different if the numbers of oxygen and 
polar hydrogen are different,then g(r) will be different,what is the
problem? I know there are many references about calculating the g(r) for
heteroatoms,please give me some comment
and/or refer me to some references.

Wei