Dear RG members,
Is it required to add counterions (Na+) to a MD system with negatively charged lipid molecules (POPG). Can I perform MD without adding counterions for my target protein?
Thanking you
Sincerely
Bikash
I'd suspect you'd have massive artifacts if you didn't neutralize the unit cell. Methods like PME include a so-called "neutralizing background plasma," but studies have shown that for heterogeneous systems like membranes, the artifacts of such assumptions are quite severe.
The overall electrostatic neutrality requirement, of aqueous solutions or suspensions calls for counterions to be present. However, do not forget that a difference exists between the physico-chemical nature of the bulk solution and that prevailingin the very near vicinity of the lipid bilayer. Without any counterions, the surface potential of the lipid/protein complex may be very high, but in addition, in absence of such counterions as Na+ or K+, the system will react in by increasing the dissociation of water molecules so that the protons immobilized by the lipid/protein surface will leave the bulk of the solution more alkaline, and this may have important consequences with regard to the pH dependance of enzymatic activity.
MD is used to analyze interactions and forms of lipid bilayers consisting of palmitoylsphingomyelin, dimyristoyl phosphatidic acid, and cholesterol different proportions.Molecular dynamics (MD) simulations of the system have is to study bilayers in the Lo state, in the absence of the negatively charged lipids.Typical cell membranes have two sheets of lipids that form a hydrated bilayer. Adsorption or desorption can take place at the interface, which in turn can energy minimized minimized for 400 time to avoid overlapping of atoms. The lipid-water interface formed is on the order of 102 mV
Thank you Dr. Andrew and Dr. Ravi for your valuable advices. Thank you very much.
Yours sincerely
Bikash
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