Hi,
I am studying the stabilization of proteins using different solvents using GROMACS. Attached is the RDF of the cation (black) and anion (red) around the protein.
I used "gmx_mpi rdf com rdf mol_com -s em.tpr -f md_Dhp_2system.xtc -cut 0.5 -cn -o radialdist_cation_Dhp_2_com.xvg -tu ns" to calculate the RDF. The plot does not show any peaks. Does this mean that the cation and anion are uniformly distributed right from 0.5nm of the protein?
Thanks.
Uniform would be g(r)=1. This is definitely not the case from your plot. I do not no much about ion distributions so I cannot tell if what you see is expected behaviour but I think you can read quite a bit from your graphs.
First of all both ion species seem to be depleted right next to the protein. Could this be steric/excluded volume? What is the effective size of your ions (maybe including hydration shell)? Then there is a first layer of cations followed by probably a second layer of anions. Does this make sense?
If you have reasonably low concentrations of ions there is no reason to expect strong peaks in g(r). Why would there be strongly prefered distances in a dilute solution. I would think your peaks are already pretty strong.
As Till mentioned, you would only get peaks in case of a dense system, in which these ions would experience strong interactions from each other. But in your case, it seems that the concentration is low, so they are more affected by the stochastic forces exerted by the water molecules than by mutual interaction. These RDF plots correspond more or less to an ideal gas.
If one looks closer, and if everything has been ok with your simulation and your sampling (the system has indeed equilibrated and you have enough sampling in calculating the rdf), it would seem that the protein's surface has a small positive charge, which has attracted the anions, leading to a Gouy double-layer structure.
Thanks Dr. Kranz and Dr. Sadeghi for such detailed explanations. The RDF plots make a lot more sense to me now. Earlier, I did not consider the effects of concentration while analyzing the plots. Through my simulations, I was expecting a double layer with the bulkier cations as the first layer.
There are just few more queries which I would like to clarify.
1. Could you please explain more on " your peaks are already pretty strong"? Can the plot be inferred as strong if the g (r) is approximately 1?
2. Does the plot mean that the both the cations and anions intercalate the protein backbone and are able to penetrate into the core of the protein?
3. Attached is the RDF of my second set of anions (acetate) with the same cation. Is it right to conclude that the acetate anions are interacting with the protein's surface much more than that of the anion 1? This combination of acetate and cation has indeed led to an increased RMSD.
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