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

[Justin Lemkul]

On 7/5/17 12:17 PM, Nidhin Thomas wrote:
> Hi Justin,
> 
> Thanks a lot for the prompt reply.
> 
> I used just 400 POPC lipids to build the lipid bilayer and when I added 150 mM KCl, it added 49 K+ and 49 Cl- to the system. Do you think these numbers are correct? Could you please tell me how I can check the correct number of ions?
> 

Look at the CHARMM-GUI output, note how it calculates volume, and pull out a 
calculator for moles/volume :)  Neutral lipids require no counterions, so 
everything you add is just the desired salt concentration.

> The size of the original system (300 POPC + 100 POPG) was (11.7480468  11.7480468  8.98 ) nm. If the size of the system is very small to accommodate the ions, how can I change the size of the system in charmm-gui ? Or should I just get the bilayer system and add ions by myself using gonion command in gromacs?
> 

IIRC you can control how many hydrating waters you get per lipid.  If you 
increase the number of waters, this will increase the volume.

-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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