[gmx-users] Calculation for number of ions

Abhishek Acharya abhi117acharya at gmail.com
Sun Aug 5 14:45:27 CEST 2018

> 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.

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