Coordination number of metal ion to oxygen of water in second solvation shell of metal

User discussions
1

GROMACS version:2022.1
GROMACS modification: No

Dear all,
I am trying to find metal ion to O(water) coordination number in the second solvation shell of metal ion using the following command:

gmx_mpi rdf -f fullmd.xtc -s fullmd.gro -n index.ndx -o rdf.xvg -cn cn.xvg.

I took 0.25 nm cutoff for finding the coordination number in first solvation shell (which came out to be 4) and then I took 0.5 nm cutoff for second solvation shell (the CN here was ~20). My doubt is that this value 20 is basically the total coordination number in solvation shell 1 and 2. To get the second solvation shell coordination number, is it fine to simply subtract 4 from 20 (i.e. 16) so that coordination number corresponding to second solvation shell is 16.?

2

Does this thread help you How to calculate coordination number??

3

Dear Magnus,
Thank you for directing me to this link. I understand the concept explained here. I am just worried if it is correct to do the direct subtraction of these average coordination numbers as I mentioned in the question to get CNs corresponding to the second solvation shell.

Kind regards,
Abhi

4

Dear user,

I recommend plotting RDF and CN in the same chart to count the number of desired atoms/molecules in the first or second shell around the target or any desired distance. The second RDF minimum is usually considered as second shell.

5

Thanks Dear rezayani, I will try doing that.