[gmx-users] acidic pH simulation

[Justin Lemkul]

On 12/14/19 1:27 AM, Iman Katouzian wrote:
> Good day,
>
> I want to simulate the behavior of my protein at different pH conditions
> including *acidic and basic values*. Can somebody suggest what should I do
> to change the pH of my system?

You don't, at least, not in GROMACS. There are constant pH methods 
available in other software like AMBER and CHARMM, but GROMACS cannot do 
such simulations. The closest you can come is setting protonation states 
of relevant residues to specify the dominant state of these residues at 
a given pH value. But since you will not have free H3O+ or OH-, and you 
cannot have dynamic protonation during your MD simulation, you cannot 
say that your simulation was conducted at a given pH value. You can only 
say that the protonation states were chosen to be representation of a 
given pH value.

-Justin

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Justin A. Lemkul, Ph.D.
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jalemkul at vt.edu | (540) 231-3129
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