GROMACS version: 2020
GROMACS modification: Yes/No
I want to calculate coordination number of water around N+ group. I first calculated area of RDF to first minimum and it gave me a wrong coordination number( my RDF is correct) . Then I used this command
gmx rdf -f file.xtc -s file.tpr -b -e -cn coord.xvg -n index.ndx -ref “group N” -sel “group OW”
But, the out put was not coordination number of water around N+.
What is the correct way to calculate coordination number?
Thanks in advance
the first coordination number is the first inflection point of the curve reported in coord.xvg
do you mean that the coord.xvg file is empty?
In alternative you can use the integral of rdf (have a look in the literature for the formula)
Thank you very much for your reply. With the mentioned command line I received this plot for (-cn coord.xvg)
I know coordination number in this level of hydration is about 13-15 but this plot is a little weird.
yes, the plot looks like how it should.
From a visual inspection of the plot, the first inflection point is around 0.6 nm and correspond to a coordination number around 13-14 (values in y-axis). You can zoom in around the inflection point to better define the value for the coordination number
Thank you very much again. your response made the way clear for me.