Setting pH in gromacs

User discussions
1

GROMACS version: 2023.3
GROMACS modification: Yes/No

How set a requisite pH in gromacs for MD?

2

If you’re talking about fixed protonation states, the common and quick way is to pass your structure through a pKa predictor like PropKa, and then - if needed, according to the output - set non-standard protonation states in gmx pdb2gmx, using flags like -his, -asp and so on.

If you want to run “true” constant-pH dynamics, i.e. with dynamically changing protonation states, you should take a look at the early implementation available from the teams in Finland & Sweden.