I have the experimental result for the zeta potential of a (g-C3N4) nanosheet, now can I relate that to the total charge of a molecule to be used in a molecular dynamics simulation?
this may be possible with some simplifications. There is model for this (Ohshima equation, for proteins in monovalent salt buffer) that may work for you.
For the relation between charge, electrophoretic mobility and zeta you might find https://www.materials-talks.com/protein-charge-determination-how-to/ of interest.
I suggest a paper I published in 2020 that compares estimation of charge on protein in aqueous salt solutions using electrokinetic measurements vs. measuring the charge via acid-base titration:
Article Determination of Protein Charge in Aqueous Solution Using El...
As you'll see, you need to select the correct electrokinetic model. You'll also see that the concept of zeta potential may not even apply.