[gmx-users] simulation in acidic condition

[ali khamoushi]

Thanks for your answers. so, I leave you with one more question. if I use
HCL ions in shape of H3O+ and Cl- instead of NaCl for neutralization, isn't
it disrupt system?

On Sat, Oct 13, 2018 at 1:46 AM Alex <nedomacho at gmail.com> wrote:

> 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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