[gmx-users] adding counter ions
OZENGIN at KU.EDU.TR
Tue Jun 12 10:48:43 CEST 2007
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.
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
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