[gmx-users] how to make the SiO2 host to be neutral ?

[Kiwoong Kim]

Hi,

I'm studying the diffusion system of some guest into zeolite structure
(SiO2) assumed to be rigid body.

My question is about making the host neutral.

I obtained the unit cell of zeolite structure from the web.

The structure exhibit net charge. (If I give some charge to Si and O which
satisfies qSi+qO=0)

In other words, the number of O is not the same as the twice of that of Si.

I guess that some residue O is necessary to synthesis the system which is
combined with a lot of identical unit cell.

How can I solve it?? I think if I continue the study with net charged
zeolite, there can exists some finite size effects.

Can I delete the residue O atoms that does not connect with Si in the
system that I made with a lot of unit cell.
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