[gmx-users] simulation in acidic condition

[ali khamoushi]

so, if I protonate my protein and then put it in neutral condition, is it
going to work? I mean should I use particular ions for neutralization?

On Sat, Oct 13, 2018 at 12:56 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/12/18 5:14 PM, ali khamoushi wrote:
> > hello everyone. I want to simulate a protein without ligand in gromacs in
> > acidic conditions. but I don't know what exactly I must do. should I add
> > HCL ions (for example) to turn neutral surrounding into acidic?
> > my protein is Insulin. and I want to see behavior of his protein in
> acidic
> > condition.
>
> If you really want to monitor pH sensitivity, you should be doing a
> constant-pH simulation. For that, you need to look for other software,
> because you can't do those kinds of simulations in GROMACS.
>
> Adding explicit HCl (which really should be H3O+ and Cl-) isn't
> appropriate either, because as soon as you have one hydronium ion in a
> simulation box, the pH is actually astronomically low (do the math and
> you'll see), and as well it's neither physically realistic nor useful.
>
> The cheap approach that people often use is to simply protonate the
> biomolecule according to the dominant state at a given pH and simulate
> it that way. It's an approximation, but it may work.
>
> -Justin
>
> --
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>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
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