I need to run a MD simulation of a protein in the cytosol and I want to reproduce experimental conditions of pH and ionic strength.
In the cytosol, K+ has higher concentration than Na+, nonetheless I have seen several works where the ionic strength was set using NaCl.
Ultimately, does it really matter which salt I am using, as long as the final value of ionic strength is the one desired?
citosol is a very crowded environment and to simulate you need at least pH, ionic strength and the free volume of the solution . This free volume depends on the eventually present non charged molecules and the size of ions. K+ has not the same size as Na+, so the activities of protein is not the same with different ions even at the same the concentration. Probably the influence is not great at low concentration but it certainly matters at the higher ionic concentrations in citosol.
What property are you after? Ionic strength and pH are bulk properties that you can control locally in your simulation by the effective concentration of these species, but if the only effect you need in your model is electrostatics, you might be better off using an implicit solvent.
On a different note, molecular simulations of anything but weak electrolytes are not trivial, so cytosol modeling will require some degree of approximation to include properly.
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