Dear all,
I am to simulate a protein in an acidic solvent, however my previous efforts failed as Rg or RMSD of the protein were not really significant.
I had used H++ to find out protonation state.
Could you please tell me any method for acidifying the solvent with reliable simulation results?
I appreciate your helps.
Regards
The approach of protonating your molecule in its dominant state at a given pH is the closest approximation you can make without actual constant pH simulations (which GROMACS can’t do). You can’t add H3O+ or OH- in any sensible amount in a simulation box, nor would they be able to cause (de)protonation of your solute as in a real system.