I have imported a system from CHARMM-GUI which includes a membrane, a sodium channel transmembrane protein, and surrounding water. I am trying to add different ion concentrations on either side of the membrane to mimic a real human neuron. For example on one side of the membrane I am trying to add a 0.015 molarity of NA on the intracellular side and a 0.142 molarity of NA on the extracellular side. I am trying to do this for moltiple ions. However the function I found for adding ions is gmx genion, but this function keeps adding a concentration of ions to the whole system. Does anyone know how to add certain concentrations of ions to a certain side of the membrane?
Dear @harshil.jegan
Does your system consist of only one membrane bilayer?
Yes with an embedded sodium channel and water on each side.
Then because of periodic boundary conditions you have only one water slab, that is, there is no one side/the other side of the bilayer, but both sides “communicate” (they are, in fact, the same side). As such, you can’t really create an ion gradient in this way. I guess you will need at least another bilayer to keep the water phases separated!
So how would I create a realistic way to model a human membrane of a neuron to find out how the transmembrane protein works.
One option could be to have two bilayers in your simulation box so that you can effectively have two water phases that are separated and can have different concentrations.
However, my opinion is that your best option is to check previous literature and see if there are any other methods or better ways to simulate such gradients, as I am sure this is not a new problem in the MD simulations field. Taking a few hours to explore and study previous published work will easily save you hundreds of hours of effort and computational time!