Hi,

I have a water simulation box with 116 water molecules. I used TIP4P water model. Now I need to calculate RDF of water-water, RDF of Oxygen-Oxygen and RDF of Hydrogen-Oxygen.

I tried to calculate RDF of water-water and ended up with the wrong plot which I did not expected.

My Index file order is like this: O “System” 1 “Other” 2 “HO4”

I used following code to calculate RDF;

gmx rdf -f traj_comp.xtc -s run01.tpr -n index.ndx -o Water.xvg and for the sel and ref I choosed option “O”

How can I used GMX RDF option to calculate RDF data correctly.

Cheers, Kal