GROMACS version: 2021
GROMACS modification: Yes
I am using Gromacs.2021 compiled on my own pc with Intel MKL and MSVC++/Intel C++ compilers. I performed an MD simulation on a spherical cluster of ~200 H2O molecules kept at the centre of a 6 nm cubic box. The simulation ran fine.
Then I calculated the radial distribution function with gmx rdf -f md.xtc -s md.tpr -n index.ndx -ref 2 -sel 2
In the index file, 2 represents SOL (i.e. all the solvent molecules). I thought this would use the centres of masses of all the H2O molecules and then create a distribution from that. The graph I got was this: image.png - Google Drive . It does not look like what I would expect at all. There are two peaks for some reason. Is it taking the O and H atoms separately for each molecule? How can I direct it to use the centre of mass?
Any help is appreciated!