[gmx-users] adding counter ions

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jun 12 02:49:54 CEST 2007

> 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 


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