GROMACS version: 2018.4
GROMACS modification: No
For anions it is simple, always CL-. For cations there is some options to choose. For example in charmm-gui membrane builder CHARMM-GUI the default option is K+, but in many GROMACS threads I saw that people use also Na+. Is there be any huge difference if you neutralize your system with a different ion or it doesn’t matter? I mostly work on membranes, so I was curious that is different ions can have an influence on for example membrane properties like area per lipid or number of hydrogen bonds or lipid etc.