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

[Justin Lemkul]

On 11/4/16 6:09 PM, Alex wrote:
> 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?
>

Counterions and bulk salt are different.  A counterion is specifically added to 
balance the net charge on the solute.  If the solute is neutral, no ions that 
are added into the bulk are counterions.  They are all bulk ions that are part 
of the ionic environment in the system.  People do this to mimic experimental or 
physiological conditions, because ions increase the dielectric of the solution 
and screen charges.

-Justin

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

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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