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

Jesse Lentz jesselnz at gmail.com
Fri Apr 19 02:24:46 CEST 2019


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
fields have OH in their respective ions.itp files, but my understanding is
that mixing molecules of different force fields is dangerous business.

How would an experienced GROMACS user add an OH- ion to this system? Thank


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