I am interested in knowing about the pH of system during simulation. Several forums have stated that .mdp has nothing to do with altering pH of the system and it got something to do with pdb2gmx.
So what would be the pH if I use pdb2gmx without adding protonation or deprotonation.
pdb2gmx protonates assuming neutral solution conditions and canonical pKa values, but this does not mean that the subsequent system has anything that you can call pH.
To alter the pH of a solution you need to add H+ ions, but the parameters for H+ ion is not available as you can not treat it classically even inside a solvent box. Is simple words, H+ ions can not be simulated classically while they are free in the solution, as far as I know).
If there is a way to simulate loose H+ in GROMACS, I am very eager to know that.
Thanks.
Sayantan: Why can't you simulate H+ if you know the charge and the mass of H+? Is there anything else you need to define? If yes, what is it and why can't you define it?
It would of course be represented as H3O+ (which then has to be fully parametrized, including charges and LJ), but the issue is that a free hydronium floating around isn't really a good representation, nor does it actually tell you anything at all about the biomolecule. Moreover, once you put a couple of H3O+ in a simulation box, your pH becomes unrealistically acidic (going by purely concentration) due to the small size of the simulation box. H3O+ and OH- have been parametrized for various force fields, but no one uses them because it's not a good physical model for anything useful.
I couldn't agree more with you, Justin. This is the main and unavoidable problem when you want to insert free H+ or H3O+ inside your simulation box.
If one wants to study the effect of changing pH using MD simulation, what should be done? Is it not possible to take pH into account in any simulation? Is there any other bypass methods?
The simplest approach is to run different simulations with different protonation states after calculating pKa values for titratable residues. This allows one to simulate the dominant state of the molecule that would exist under certain solution conditions.
The more elegant approach is to actually do constant pH simulations. The CHARMM software can do this. See work by Brooks, Shen, et al.
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