[gmx-developers] Computing the density of water around water

David Cerutti dcerutti at mccammon.ucsd.edu
Tue Apr 11 01:12:19 CEST 2006


    I know that one can get g2(r) (radial distribution) information from a 
simulation of identical particles by looping over all particles i and 
making a nested loop over all particles j < i.  Thus, one can compute 
(1/2)N^2 interactions from each snapshot for computing the histograms that 
go into each g2(r).  However, I'm not sure if one can do this for the 
three-dimensional density calculations.
    If I simply want to plot the three-dimensional density of water oxygen 
atoms around a particular water molecule, is it OK to do a simple 
simulation of water (no constraints, no particle fixed at the center) and 
then analyze each snapshot by putting every water molecule i at the center 
and considering the oxygen atom of every other water j < i in my density 
histogram?  This would increase my sampling by N/2 times, and in my 
simulations N is 1728!  It seems like that should be all right, but I just 
wanted to check.


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