I’m having difficulty in trying to generate an unnormalised RDF. I have used the command below but it returns with an error message.
gmx rdf -f Traj.xtc -s Input.tpr -n index.ndx -surf mol -bin 0.02 -o RDF.xvg -cn Nlig.xvg -seltype mol_com
So as you can see I want to calculate the unnormalised RDF between my protein and COM ligand. In the error message it says -ref should contain atoms. My index file does contain atoms e.g. it says there are 6615 atoms in the group but it does not seem to work. Please may someone guide me in solving this problem?