# RDF Calculation of water **URL:** \ **Category:** User discussions\ **Tags:** mdrun, analysis-tools, simulation-setup\ **Created:** [November 6, 2022, 10:44pm UTC](https://gromacs.bioexcel.eu/t/rdf-calculation-of-water/5186 "2022-11-06T22:44:14Z")\ **Posts on this page:** 1\ **Page:** 1
**Author:** ![Kal](https://avatars.discourse-cdn.com/v4/letter/k/9de053/32.png) [@Kal](https://gromacs.bioexcel.eu/u/Kal)\ **Post date:** [November 6, 2022, 10:44pm UTC](https://gromacs.bioexcel.eu/t/rdf-calculation-of-water/5186/1 "2022-11-06T22:44:15Z")
GROMACS version:2021.4 GROMACS modification: No Here post your question 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 following 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 ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/1/1d1c41a5223f92ecd1cf3e436b95c1b81813bbf2.png)