Basic questions about constant pH simulation

User discussions
1

GROMACS version: 2019.3/intel-2018
GROMACS modification: Don’t know
Here post your question

Hi, I’m a beginner at Gromacs and I want to use Gromacs to run MDs at different temperatures, pHs, and ionic strengths. I’m looking at your constant pH simulation page where it is said

The ideal situation would be to have a constant-pH algorithm to perform the MD simulations. However, conventional explicit-solvent MD algorithms cannot do that, since they’re constant-H+ algorithms.

I was just wondering i) why it’s ideal to have a constant-pH to perform MD, and ii) why constant-H+ is not equal to constant-pH? Apologies if this question is too basic.

Many thanks.

2

A solution that exists at a given pH means there are dissociable protons around, and that groups can change their protonation states as a function of their chemical environment and the dynamics in the system. Such a situation is not possible with conventional MD, because it involves dynamic changes to the topology, which requires a specific technique called constant-pH MD, which allows the topology to change over time. This is “ideal” in the sense that it reflects physical reality.

As noted at the linked page (please note this is a very old document and constant-pH methods are not actually formally supported by GROMACS but a new implementation is on the way), even at extremely acidic pH, the number of H+ that would exist in a typical simulation box would be effectively zero. So one does not worry about changes in protonation state; we call that constant-H+ (or constant protonation state) because we treat all species in the system in their predominant state at that pH (given the pKa values of titratable groups and take that as representative of the system at equilibrium, and the protonation states do not change.

1 Like
3

Thank you for your answer.

So as a summary, can I understand it in this way: if we want to change pH experimentally in the lab, we add acid into the solutions. Gromacs does a similar thing, but instead of adding acid (i.e. H+) to the simulation environment, we change the protonation states of the proteins we want to simulate (such as adding charges to proteins). This can be achieved by pdb2pqr. In this way, the protonation states of all the species in the system will maintain the same from the very start of the simulation till the end of it.

Hope they make sense to you?

4

In GROMACS, the tool is pdb2gmx, but otherwise yes, this is generally the idea.

1 Like
5

Thank you!

6

Hi, can I ask a follow-up question related to pdb2gmx?

I learnt that pdb2gmx allows me to add hydrogen to the side chains of my proteins, and can “prompt the user to select which kind of LYS, ASP, GLU, CYS or HIS residue is desired.” as pointed out in the gmx pdb2gmx web page.

So if I understand it right, pdb2gmx will find those five amino acids in my protein and add hydrogens to them according to the protonation states I set? Perhaps this question is out of my nativity, but what if my protein doesn’t contain any of those five amino acids mentioned above (I don’t know if it’s possible) how could I set the protonation states then? Hope this question makes sense.

7

If your protein does not contain amino acids with titratable sidechains, then the only protonation states you can choose are those of the N- and C-termini.

1 Like
8

Thanks very much!