OZGE ENGIN wrote:
Dear Mark,
I had read papers about the simulations of charged systems. You' re right. In these studies, the distance between the charged residues have been controlled during the simulation.
In this respect, you suggest me not adding counter ions to the system:
Providing the distance between the oppositely charged residues :-) is not far apart than the optimum which means that they are located at such a distance that they have the ability to cancel each other.
If they're already 3 angstrom apart you won't want counter ions, but if
they're 3nm apart you will.
Mark
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