[gmx-users] Counter-ion in a initially neutral system

Alex alexanderwien2k at gmail.com
Fri Nov 4 23:10:10 CET 2016

Dear gromacs user,

In my simulation (solid surface + peptide in aqueous solution) I have a
heptpeptide in which contains 2 times Glutamic acid (negatively charged)
and one Arginine(positively charge) and one Lysine(positively charge), so,
as you see the heptpeptide is charge neutral in general(the whole system is
also neutral) despite having charged amino acid.
However, In such situation I see sometimes people add also "Na + Cl" as
counter-ion in the system, I do not know why!, I was wondering if it is
really necessary to do that or make sense, as It is neutral initially?
What if I do not add them?
How can I see their effects quantitatively?
How can I find out if I need the Counter-ions or not?

By, the way, the goal of simulation is to calculate the PMF of
heptapeptide-surface interaction* in *physiological condition by US.

Thanks in advance.

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