Hey all, I am trying to examine couplings between Mg+2 ions and a peptide with a -5 charge. I would like to optimize couplings and have considered using a +1 charge from the system. I read that GROMACS can do this and that in theory it should have the same effect as adding ions but it is not standard practice. For future simulations I plan to increase the [Mg+2] and am worried about couplings from Cl- if I were to use Cl- to neutralize the excess positive charge. Is it ok to use the system to neutralize these charges? Or is that considered a bad experimental design?
Thanks for you feedback! Arden Perkins
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