GROMACS modification: Yes/No
I want to simulate OH- and H+ diffusion in polyelectrolyte using OPLS-AA force field. But, I could not find parameters of these ions in ion.itp of gromacs files. What should I do for that?
Thank you very much
If the parameters are not defined in the available ff, you need to parameterize it using QM tools. Check in the ff file whether these atoms are available or not. or use gmx insert-molecule tool to insert
Thank you very much for your response.
This is not a straightforward issue, as both OH- and H+ are not as simple as they seem. They both will have well defined hydration structure, and in fact, H+ doesn’t exist in solution; it’s H3O+. The proton is also quite quickly exchanged between water molecules, so studying such a system assuming a discrete H3O+ entity is flawed. OH- is similar. These are probably systems that would be better handled by ab initio MD. The classical assumptions break down.