[gmx-developers] Computing the density of water around water
David Cerutti
dcerutti at mccammon.ucsd.edu
Tue Apr 11 01:12:19 CEST 2006
Hi,
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.
Thanks,
Dave
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