[gmx-users] How the pH is reflected in Gromacs?

[ZHANG Cheng]

Dear Gromacs,I am simulating pH 4 condition. I interactively assign the protonation of chargeable residues of a protein based on PDB2PQR results by setting pH=4 in the "pKa Options" (http://nbcr-222.ucsd.edu/pdb2pqr_2.1.1/).


I do not add citrate or acetate molecules to the simulation box. So if the pH 4 condition could still be reflected?


Thank you.


Yours sincerely
Cheng