Hi,
I was wondering if there was a way to build a system with hydronium ions similarly to how salts can be included into a system? For example in emc_v9.4.4/examples/tutorial/bulk/setup.esh, there are salts, Na+ and Cl-. Would there be a way to put in hydronium ions instead of Na+?
Dear user,
One could, provided the force field you use supports a hydronium ion. I would assume a SMILES would look like HO(H)H. The force field definition should then take care of the assignment of the partial charges, such that the overall net charge of the ion is +1. An alternative — and rigorously more correct — representation would be H[O+](H)H.
Thank you! I was not entirely aware that you can write out the hydrogen in SMILES