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

Based on your pKa prediction by PDB2PQR, set protonation state for Asp/Glu/His/Lys/Arg accordingly. That is all you can do in GROMACS. Constant pH MD should be used if you want to make your simulation pH responsive. Cheers On Wed, May 17, 2017 at 11:18 AM, ZHANG Cheng <272699...@qq.com> wrote:

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

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