[gmx-users] Number of ions in Anionic lipid system- Charmm-GUI

[Justin Lemkul]

On 7/4/17 9:20 PM, Nidhin Thomas wrote:
> Dear GROMACS Users,
> 
> I have created a lipid bilayer system (300 POPC + 100 POPG) using CHARMM-GUI.
> I want to include 0.150 M KCl in the system. When I use the option in charmm-gui, it gives 98K+ ions and -2 Cl ion. But when I calculated the number of ions using the size of simulation box, I am getting 98 ions.
> 
> Can anyone tell me what I should do to get the exact number of ions in the system?
> 

CHARMM-GUI calculates an excluded volume due to the solute (protein, nucleic 
acid, lipids, etc) so using the total box volume is incorrect when calculating 
the number of ions in solution.  The result you're getting tells you that your 
box is too small (insufficient solvent volume) to achieve 150 mM KCl.

> Would it be correct if I first neutralize the system using 100 K+ ions and then add 0.15 M KCl ions (49 K+ and 49 Cl-) in the system?
> 

No, because then your effective concentration is much higher than what you want.

-Justin

-- 
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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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