I would like to model the development of AFm phases in low water environments with the addition of metakaolin, but i don't know how to input non crystalline materials in the GEMs software.
First you need a good database, I recommend the CemData distributed by EMPA. You've various ways to tackle this modeling problem, but probably two of them are the most suitable for the application. The first one (not my personal favorite) is to input the "recipe" of the system in terms of oxides (CaO, Al2O3, Fe2O3, etc). You can take the XRF analysis of your cement, metakaolin, limestone, fly ash and whatever you want, and input the addition of the different oxides according to the blending design. Please take into consideration that GEMS has no way to model de reaction kinetics of your glassy phases, so either you input this data as a degree of reaction (as a weighting factor to the quantities you input) or you just calculate quantities at equilibrium, considering 100% of reaction of the amorphous phase.
The second way (which I prefer to keep mental consistency of the model) is to do it in term of phases. In this case, you input your cement composition as C3S, C2S, C3A, etc. You can include limestone as CaCO3, etc. The trick is how to input the SCMs (FA, MK). You can create a new "phase" in the Compos tab of the database editor window. Attached is a picture of how a pure metakaolin composition should look like. For a FA, you can do in an analog way using the atomic composition of the glass fraction. The created phase will be imported to your project and will be available to use on it (as a single reaction or a Process calculation, GEMS will associate "MK" or whatever name you define as this phase).
Please note that the phases created in this way will "react" completely when included to the system, so you need to control the kinetics on top of this (same issue that with the first strategy). The nice thing is that now you'll have a MK phase in your recipe menu, which you can add to the system in the same way as the original phases contained in the database.
For further details on how to do this, I recommend you to consult the highly detailed and useful help file of the software. I hope this helps you and good luck with your modeling!