[gmx-users] simulation in acidic condition

Sat Oct 13 01:18:27 CEST 2018

I am not aware of any forcefield with an established H3O+ ion model (and it
is a pretty complicated subject), so you would need to develop the
hydronium ion model yourself and justify its use instead of things like
KCl/NaCl.

Alex

On Fri, Oct 12, 2018 at 4:27 PM ali khamoushi <khamuoshia at gmail.com> wrote:

> 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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