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

Justin Lemkul jalemkul at vt.edu
Fri Apr 19 02:55:12 CEST 2019

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 A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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