[gmx-users] simulation in acidic condition

[ali khamoushi]

I deeply understood your explanation. so, if first I protonate protein,
then neutralize charge of protein with ions like NaCl and run MD
simulation, is it gonna probably work and give me answer? I just wanna know
that is my protein going to denature in this condition (which I prefer call
it so-called acidic PH condition) or not?

On Sat, Oct 13, 2018 at 1:18 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/12/18 5:43 PM, ali khamoushi wrote:
> > 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?
>
> Plainly, there is no such thing as "pH" in an MD simulation. pH refers
> to the -log[H+], of which there are none in the MD simulation. So you're
> not putting anything into a "neutral condition." The protonation state
> is what you set it to be. If that reflects the dominant protonation
> state at some real-world pH value, then that's all it is. The rest of
> the solution doesn't have a pH.
>
> Neutralization with ions is a separate issue. But neutralization of
> charge is not the same as "neutral pH."
>
> -Justin
>
> > 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
> >>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Assistant Professor
> >> Virginia Tech Department of Biochemistry
> >>
> >> 303 Engel Hall
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalemkul at vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==================================================
> >>
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
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