[gmx-users] Calculation for number of ions

[Abhishek Acharya]

> 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.
>

Is there a reason to assume that they should not interact ?

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.
>

It is not clear as to what you will achieve by constructing the system this
way. Normally, adding neutralizing ions and additional ions to a given
conc. should be enough. Assuming correct simulation parameters, your system
should sample the accessible states as it would in a real life protein. So,
I don't really see the point in adding extra 'shielding' ions.

Also, practically speaking to, if you add the extra shielding ions after
neutralization, the system will have a high net negative charge. So you
would need to further add neutralizing positive charges; and we are back to
the square one. Even, with PME that introduces a background neutralizing
charge, but that is known to produce artifacts in case of inhomogenous
systems such as membranes.

>
> I tried physiological conc of 0.154 mole/L using genion command but it adds
> equal number of Na and CL ions.
>
> This will only add NaCl to the system  that makes up a concentration of
0.154 M that is over and above the neutralizing counterions.