You are basically asking to help you debug a matlab script entirely imagining how it computes the Nmolec and waternumber variables. I believe Prof. Charles Francis Xavier is the only one who can help!
Could you post the header of the dump you pass to MATLAB?
That’s not correct. LAMMPS will assign a molecule index for each ion, because the same atom_style is shared by all the atoms.
As a side note: if you want to make life easier for people who may have a marginal interest in helping out, you should formulate your problem in a concise, logical way, and share the relevant information. Also, please make the effort to read the forum guidelines.