[gmx-users] Beginner question -- How to model an OH- ion using OPLS/AA.

[Jesse Lentz]

Justin,

Thank you for your answer! I believe I'm on the right track now.

Sincerely,
Jesse

On Thu, Apr 18, 2019 at 8:55 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/18/19 8:24 PM, Jesse Lentz wrote:
> > Hello,
> >
> > I'm a beginner, struggling to learn GROMACS to the point where I can
> > simulate a simple system of two ions in an organic solvent. If this
> mailing
> > list is not the right place for these kinds of newbie questions, please
> let
> > me know (I'm sure this will not be the last place I get stuck!).
> >
> > I was able to obtain .itp files of my solvents (published by researchers
> > who have worked with them in the past), and I was able to add an Li+ ion
> to
> > the simulation box using gmx-genion. I'm stuck trying to figure out how
> to
> > add an OH- ion. OPLS/AA does not have OH- in its ions.itp file, which I
> > believe implies that I'm responsible for assembling/finding my own OH-
> > topology. However, OPLS/AA does have two atom types (opls_434 and
> opls_435)
> > which appear to be specifically meant for the O and H atoms in OH-, which
> > implies that this is already a solved problem. I noticed that other force
>
> Indeed, the parameters are in the literature and a reference is given.
> The documentation within the OPLS-AA force field is pretty sparse,
> though, which makes obtaining topologies difficult.
>
> > fields have OH in their respective ions.itp files, but my understanding
> is
> > that mixing molecules of different force fields is dangerous business.
>
> Never mix force fields :)
>
> > How would an experienced GROMACS user add an OH- ion to this system?
> Thank
> > you.
>
> Coordinates for two atoms connected by a bond of a given distance can
> easily be created by hand. Place the O atom at (x,y,z) and H at
> (x+r,y,z) and you're done.
>
> gmx insert-molecules is used for inserting polyatomic species. gmx
> genion is solely for monoatomic ions.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
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>
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>
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