A pH of 5.5 would mean 3.16*10^-6 mol/L of H+ concentration. When I convert it into number of molecules per cubic Angstrom, it would be 1.9*10^-9 molecules. It means the box length (assuming cubic) should be around 800A for one H+ molecule. This is too huge simulation box.
In general, how is this problem statement addressed in MD simulations? How do we consider such pH range with feasible simulation parameters?
I want to simulate a solution of organic acids in water system, with different pH ranges.
Normal MD does not simulate changes in protonation during the trajectory. pH-dependent protonation of the titrable groups is assessed and assigned when preparing the molecule for MD, but does not change during the run. To allow protonation during the simulation, special methods are used
e.g.
https://www.nature.com/articles/srep22523
https://www.ks.uiuc.edu/Research/namd/2.14/ug/node80.html
https://www.frontiersin.org/articles/10.3389/fmolb.2022.922361/full
Article Dataset showing the Impact of the Protonation States on Mole...
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62838fef43d1f07da52f2d56/original/best-practices-in-constant-ph-md-simulations-accuracy-and-sampling.pdf
@Annemarie Thanks for the reply. However, I am not looking for a pH change. What I am trying to simulate is a constant pH solution. But, the required box dimensions are huge. So, I want to know if there is any other alternative.
Another approach is to use a constant pH MD (CPHMD) method, which includes explicit water molecules and ions to represent the solvent environment. In CPHMD, the protonation state of titratable groups is determined by the pH of the system, which is controlled using a pH replica exchange technique. This method can also account for the effects of ionization on the structure and dynamics of the solute and solvent molecules.
Additionally, choosing an appropriate force field that accurately represents the solute and solvent molecules and their interactions is crucial. Many force fields have been developed for simulating organic molecules and water, and some of them include parameters that can be tuned to match experimental data, such as pKa values.
Overall, simulating a solution of organic acids in water system with different pH ranges can be challenging, but with careful consideration of simulation parameters and appropriate methods, it is possible to obtain meaningful results.
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