[gmx-users] Calculation for number of ions

Justin Lemkul jalemkul at vt.edu
Sun Aug 5 14:39:41 CEST 2018

On 8/5/18 6:35 AM, Archana Sonawani-Jagtap wrote:
> Hi all,
> I want to run simulation of GPCR in POPC bilayer, but the GPCR N-terminal
> is very flexible and negatively charged whereas the ICL's and C-terminal is
> highly positively charged. Thus, the they interact with each other during
> simulation.
> So, now I want to shield the negative charges of ICL's and C-term by adding
> ions near this region after neutralising the system. Is there any way to
> calculate the number of ions required for shielding.
> I tried physiological conc of 0.154 mole/L using genion command but it adds
> equal number of Na and CL ions.

You shouldn't simply add more ions of one type to your system. Doing so 
will create a net charge that is then balanced by the PME neutralizing 
plasma, but has been proven to induce artifacts, especially in membrane 

genion has determined that your overall system is net-neutral, and as 
such, adds an equal number of positive and negative charges to achieve 
the concentration you request. If ions actually do interact in the 
manner you believe, they will accumulate there over time during MD such 
that the local concentration of Cl- ions is higher in a subset volume of 
the system. There is nothing you should do to attempt to predispose the 
system to this behavior.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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