[gmx-users] simulation in acidic condition

[Alex]

Noone knows if "it is gonna probably work." Justin simply suggested the
only way to modify pH in this type of simulations. You can certainly use an
excess of appropriate ion types added to the solvent to neutralize the
system overall. Whether it gives you any answers we don't know.

Alex

On Fri, Oct 12, 2018 at 4:07 PM ali khamoushi <khamuoshia at gmail.com> wrote:

> 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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