Questions on detecting correct species and reaction route in Ca

Dear developers,

I am using reacnetgenerator to analyze the system containg Ca ions and SiO4 anions with water molecules. I want to find the reactions between the Ca ion and SiO4 anions. I found that the coordination number of Ca is not correct, which is no more than 4 in the results of the reacnetgenerator. in fact the coordination number of Ca is between the 4 to 7 with an average of 6.

In addition, there is a lot of the reactions between the water molecules, which is not the concerned reactions. Is there any methods to precludes these reactions? The attached is the initial structure. Thanks so much!
[Ca_Si_0.67.cif.txt](https://github.com/tongzhugroup/reacnetgenerator/files/9104334/Ca_Si_0.67.cif.txt)