GROMACS version: 2018.4
GROMACS modification: Yes/No
In the process of MD simulation, the first step of converting pdb to gmx ask to select the type of N terminal and C terminal of the amino acids. The options are as NH3+, NH2 and COO- and COOH for the N terminal and C terminal respectively. Is there a specific reason to select the terminals as NH3+ and COO- and does it change with the force field we are using?
Chemically speaking, these are the dominant states at neutral pH, which is what one usually simulates for biological systems. This is not something that depends on force field, it’s a simple matter of chemistry.