SiO2 Nanocluster formation inside a carbonate simulation box

I do not understand what you mean by a "nanocluster".
Are you trying to create a small crystal of SiO2 and surround it by carbonate?
Are you trying to create a new crystal composed of a uniform mixture
of SiO2 and carbonate? (..assuming that's possible. This is not my
area of expertise)

Or is this an amorphous mixture (not a crystal)?

You can make crystals easily in moltemplate, but amorphous mixtures
require a simulation to position the molecules/atoms in a physically
realistic way. (This would be true for any molecule builder.)

If you reply, it helps to include a small sketch or picture of what
you want to build in your email.

I am currently unable to receive messages posted to the lammps mailing
list (I need to fix this problem). So, for now, please also email me