OZGE ENGIN wrote:
Hi all,
My peptide contains two adversely charged residues. I use PME option for the
investigation of electrostatic interactions within my system. The total charge
of the box must be neutral. Since the system contains adversely charged
residues, is it still necessary to add counter ions into the system?
"adversely charged" doesn't mean the same thing as "oppositely charged" :-)
While overall periodic cell neutrality has been achieved here, you will
still have separated charges that will attract each other, potentially
distorting your equilibrium state. In a real system, each of these
residues would likely have a counter-ion present closer than the other
residue - but of course you know how far apart these residues are, don't
you?
Mark
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