[gmx-users] how we can add these ions depends on precise physiological concentration?

[Justin Lemkul]

On 1/5/19 8:17 AM, milad bagheri wrote:
> Dear researcher
> As we know, we add only specific ions including Na and Cl to simulation box
> for conducting molecular dynamics simulation. The question is raised is why
> we don't add other ions to simulation box that are existed in the cell
> environment, for example, phosphate or potassium?
> It is reasonable if we add all the ions to MD box? If your answer is yes,
> how we can add these ions depends on precise physiological concentration?
> best Regards

There are two main issues here. Most species are at concentrations so 
low that you may only have one ion floating around in your box, and it 
will be impossible to obtain ergodic sampling of that ion. If you want 
more ions, you'll have to expand to huge, impractical boxes to encompass 
enough volume.

The second issue is that most additive force fields are insufficiently 
accurate to distinguish the effects of different ions, e.g. I wouldn't 
expect success if someone tried to compare the effects of one Ca2+ ion 
against one Mg2+ ion (which would be a likely scenario in most 
biomolecular MD). The force field representations just aren't precise 
enough.

-Justin

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Justin A. Lemkul, Ph.D.
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