Hi
I want to calculate the density (head, tail, and water) from the center of my system. so I use this order:
gmx rdf -f micelle.gro -s md.tpr -o rdf.xvg -n index.ndx -ref 0 -sel 7
(0 is the system group and 7 is my head group)
after the calculation of Gromacs, you can see the g(r) on the y-axis but I want the number of density instead of that. i am completely confused what is the difference between g(r) and the number of density when we use RDF (when our y-axis is g(r) and when it is “number of density” and what do they mean ?)
my ideal graph is attached.
Best regards,
Shiva