GROMACS version: 2021.4
GROMACS modification: No
Hi, I’m quite new to Gromacs (and I have very limited knowledge in computational chemistry), and I’ve got an assignment to examine the alkaline tolerance of a bonded protein-protein complex. I’m wondering if this is something that can be done with Gromacs.
So my plan is to run the simulation twice, with the same protein-protein complex, but at different pH values. I’ve done some research, and it seems that it doesn’t make sense to change the pH value directly (and I have no idea whether that can actually be done), rather, we have to change the protonation states of the system.
If this is the way to go, then how do I change the protonation states of the system? I’m not sure whether I should change the protonation state of the solvent, the complex, or some part of the complex. If I’m to change the protonation state of the complex, should I change the protonation states of the terminals, or every residue in the complex? (And I have no idea how to actually change them.) I found a -ter flag in pdb2gmx but I’m not sure that’s what I need to set.
And after the simulation, how can I examine the alkaline tolerance of the complex? My plan is to simply compare the bonding energy of the complex, but I’m not sure that’s the right thing to do.
Thanks! Any comment, or any pointer to similar topics will be highly appreciated. I’m completely at a loss here…