# Extracellular space - no counterions?

**URL:** <https://gromacs.bioexcel.eu/t/extracellular-space-no-counterions/8687>\
**Category:** User discussions\
**Created:** [March 24, 2024, 3:58pm UTC](https://gromacs.bioexcel.eu/t/extracellular-space-no-counterions/8687 "2024-03-24T15:58:04Z")\
**Posts on this page:** 4\
**Page:** 1

<div class="post-metadata">

**Author:** ![stianale](https://avatars.discourse-cdn.com/v4/letter/s/71c47a/32.png) [@stianale](https://gromacs.bioexcel.eu/u/stianale)\
**Post date:** [March 24, 2024, 3:58pm UTC](https://gromacs.bioexcel.eu/t/extracellular-space-no-counterions/8687/1 "2024-03-24T15:58:04Z")

</div>

GROMACS version: conda  
GROMACS modification: Yes/No

Hi,

I have a protein that binds dsDNA, but this happens in extracellular space. Would it thus make sense not to add counterions in GROMACS simulation?

---

<div class="post-metadata">

**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [March 25, 2024, 7:47am UTC](https://gromacs.bioexcel.eu/t/extracellular-space-no-counterions/8687/2 "2024-03-25T07:47:22Z")

</div>

There are ions in the extracellular space as well. But the concentrations are not the same as inside cells.

---

<div class="post-metadata">

**Author:** ![stianale](https://avatars.discourse-cdn.com/v4/letter/s/71c47a/32.png) [@stianale](https://gromacs.bioexcel.eu/u/stianale)\
**Post date:** [March 25, 2024, 8:53am UTC](https://gromacs.bioexcel.eu/t/extracellular-space-no-counterions/8687/3 "2024-03-25T08:53:21Z")

</div>

Thanks for the quick reply.

My bacteria are pathogens, having a transmembrane protein that binds dsDNA in extracellular space. This may be in the throat of humans, mucus of fish, etc., so I am not sure what ion concentration (or no ions, if that is appropriate) to use in my simulations.

For the record, I just used the tutorial.ipynb (under [Introduction to Membrane-Protein Simulation — GROMACS tutorials https://tutorials.gromacs.org documentation](https://tutorials.gromacs.org/membrane-protein.html)) for my docked protein-DNA complex.

Best regards

---

<div class="post-metadata">

**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [March 25, 2024, 10:07am UTC](https://gromacs.bioexcel.eu/t/extracellular-space-no-counterions/8687/4 "2024-03-25T10:07:22Z")

</div>

Firstly, you almost certainly want counter ions to neutralise the system, at least.

Human airway mucus also contains ions, see e.g. [Physicochemical properties of mucus and their impact on transmucosal drug delivery - PMC](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5744044/). I presume that the mucus salt concentrations are different between human and fish.

So, I would either use as realistic salt concentrations as possible, or clearly state (in the publication/presentation/poster) that you have not used physiological salt concentrations and why you have assumed it not to be important. In many cases it may not make a large difference if you use physiological salt concentrations or not.