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

Nidhin Thomas nidhin.thomas0624 at gmail.com
Wed Jul 5 18:17:37 CEST 2017

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?

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?


Nidhin Thomas

>> 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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