GROMACS version: 2020
GROMACS modification: Yes/No
Dear all
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?
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)
Best regards
Alessandra
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.
Hi,
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
Best regards
Alessandra
Please could you shed more light to me on the specific region to be consider as the inflection pont in coord.xvg file, and also the coordination number value?
Regards
In the figure I have uploaded in this question at 0.5 nm, there is a turning point. Actually, you need to zoom in to find it. The turning point is the first minimum of RDF. At a desired distance you can count the number of neighboring atoms, molecules, …
@mj.rezayani Thank you for the quick reply.
Please, in my case here how can I get the coordination number?
The file is obtained from rdf of CO2 round anion.
Regards.
You should zoom in till reach a plot like I attached Here. This is the CN of Br- around N+ (right axis). I recommend plotting RDF and CN in the same chart to count the number of desired atoms/molecules in the first shell around the target or any desired distance. I guess, in your case, there are 10-20 CO2 molecules around the anion.
Best
