GROMACS version: 2023.3
GROMACS modification: No
Dear all
I’m working on a system consisting of a graphene sheet with Li⁺ ions and ethylene carbonate (EC, resname EC) molecules distributed above it.
Now I would like to calculate and compare the coordination number (CN) of EC molecules around Li⁺ ions at the interface (close to the graphene surface, e.g., z < 2 nm) and in the bulk region (z ≥ 2 nm).
I’ve tried using gmx rdf -cn to compute the CN between Li⁺ and the carbonyl oxygen (atomname O2) of EC, but I couldn’t find a way to spatially filter the Li⁺ ions (e.g., based on their z-coordinate).
Is there a way to calculate CNs for only those Li⁺ ions that are located near the interface vs. in the bulk? Can this be done using GROMACS tools, or would I need to use an external script?
Any help or suggestions would be greatly appreciated. Thank you!