GROMACS modification: Yes/No
I want to run molecular simulations of protein molecules at 55°C at pH 8.0. But I don’t know how to adjust the pH of the solution in gromacs. Could you tell me the specific steps?
Or, just add water to the box, protonate the protein, and then neutralize the system charge with NA/CL, can it simulate the state of the protein at pH 8.0?
This is a reasonable approximation. Any attempt to add explicit H3O+ or OH- would lead to extraordinarily high concentration, and since protonations cannot change in classical simulations, would be meaningless in any case. Constant pH simulations are a different matter, and titration events can happen, but GROMACS does not support such simulations.
thank you for your reply.
And will gromacs automatically protonate proteins? If I submit a protonated protein at pH 8.0 as an input file, gromacs will automatically change its protonated state, or keep the submitted protonated state in the simulation.
you can use the preprocessing tool gmx pdb2gmx
to assign/to select the protonation state of residues.
Read more here on the setting and default for gmx pdb2gmx gmx pdb2gmx — GROMACS 2021.3 documentation