How to calculate the number of hydroxide and water molecule respectively in system?

Hi, I have a system including cations, hydroxide ions and water molecules, using ReaxFF potential published in DOI:10.1021/acs.jpcb.8b01127 by van Duin.

I want to calculate the number of hydroxide ions and water molecules to comfirm that if reaction has happened during stimulation. I’ve tried reax/species command but they can not distinguish OH- and H2O, even giving some “H2O2” or “Cation+ OOH” species.

Can anyone suggest me a proper way calculate/distinguish hydroxide and water molecule? I could use MATLAB post-processing as long as there is a way to distinguish the component in a water/ion system. Thanks!

Songlin Li
Ph.D. Student,
Technion, GETP & TEEM lab

What fix reaxff/species computes as bounded fragments are the fragments that are found in the simulation for the given cutoff parameters. This is what is computed. Now you may need to tweak those settings for your specific system. Please also note, that the results can largely depend on the settings for averaging. While averaging can help to remove some noise, too much averaging can also produce unphysical results (same as with a trajectory of averaged positions). It also will change the neighbor list settings and thus can negatively affect the physics of the simulation (please see the corresponding note in the documentation).