[gmx-users] adding counter ions

[OZGE ENGIN]

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. 

Thank you...

Ozge Engin



-----Original Message-----
From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Date: Tue, 12 Jun 2007 10:49:54 +1000
Subject: Re: [gmx-users] adding counter ions

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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