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Ions concentration
- roshanak
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6 years 4 months ago #7458
by roshanak
Ions concentration was created by roshanak
HI
I have a question about the article of "Coarse Grained Model for Semiquantitative Lipid Simulations" that published in 2004. In a part of this article I read this sentences: "Given the short-range nature of the electrostatic interaction in our model, the coarse-grained ions are expected to model realistic ions in the limit of moderate to high ionic strength only (above 0.1 M). Although optimized for sodium chloride, the CG ions could be used for other salts as well."
My question, that's: Is this means that lower concentration of ions is ineffective with martini model? and why? Is this because of screening effect of ions by water and being short-range electrostatics?
would you please explain this further?
I have a question about the article of "Coarse Grained Model for Semiquantitative Lipid Simulations" that published in 2004. In a part of this article I read this sentences: "Given the short-range nature of the electrostatic interaction in our model, the coarse-grained ions are expected to model realistic ions in the limit of moderate to high ionic strength only (above 0.1 M). Although optimized for sodium chloride, the CG ions could be used for other salts as well."
My question, that's: Is this means that lower concentration of ions is ineffective with martini model? and why? Is this because of screening effect of ions by water and being short-range electrostatics?
would you please explain this further?
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- riccardo
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6 years 4 months ago #7459
by riccardo
Replied by riccardo on topic Ions concentration
If you use reaction-field for the treatment of electrostatic interactions, you have explicit electrostatics up to the cutoff, hence the short-range nature of the electrostatics (as opposed to, for example, PME).
What I think is meant in that sentence is that, if you have too low concentrations (< 0.1 M) in your systems, the approximation of the short-range treatment of the electrostatics may impact your effective concentration. This means that below < 0.1 M the concentration you are simulating may not strictly represent the concentration you think (i.e., the conc of ions you put in the box) you are simulating.
Besides this, I would recommend to consider using the polarizable version of Martini and PME (long-range treatment of electrostatics) if you expect the electrostatic interactions to play a big role in your systems. Or, at least, test the effect of treating the electrostatics with reaction-field vs PME for your system.
What I think is meant in that sentence is that, if you have too low concentrations (< 0.1 M) in your systems, the approximation of the short-range treatment of the electrostatics may impact your effective concentration. This means that below < 0.1 M the concentration you are simulating may not strictly represent the concentration you think (i.e., the conc of ions you put in the box) you are simulating.
Besides this, I would recommend to consider using the polarizable version of Martini and PME (long-range treatment of electrostatics) if you expect the electrostatic interactions to play a big role in your systems. Or, at least, test the effect of treating the electrostatics with reaction-field vs PME for your system.
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