Dear researcher
Most MD studies are performed for extracellular conditions where NaCl concentration is high, while we are trying to perform MD for some intracellular molecule, where K, Mg, HPO4 and HCO3 is much higher than Na and Cl.
The question is how you would adjust your system for these conditions?
best Regards
thanks professor @John Liebeschuetz for response this question
Dear Milad, So, as far as I understand it , it is usually only necessary to add ions to the simulation box to exactly cancel out the overall charge that resides on the protein after your modelling software has assigned the amino acid side chains to their standard ionisation state at physiological pH. If the total charge is 0 then you probably need add no ions at all. But it is important that the system as a whole (protein, solvent, ligand, co-factors and ions) be electrically neutral. Since all we are doing is adding a neutralisation charge in a realistic way, it makes sense to use the simplest ions possible that are present in the cell environment- hence the use of Na and Cl.
The exception to this will be cases where phosphate or potassium, sulphate or other ion, play an important role in the protein's structure or function. However in such cases those ions will almost certainly be already present in your starting PDB structure and you can just leave them in place for the simulation.
I hope that helps. I should add that there are people more experienced than I in MD, and they may have a different viewpoint. Having said that the guidelines I've put above are what I use and , so far, they haven't led me into gross error.
You are asking the right questions, and making sure you don't make errors that affect your results. That is commendable
best
John
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