Since the framework.def of IRMOF-1 only contains the parameters of the organic linker atoms, my guess is that the Zn are ignored(fixed) during the simulation. So my question is "is it an approximation due to the lack of reliable parameters of the bonded interations between the Zn and organic atoms?"
One more question, the movie of the all components pdb showed that the framework atoms didn't move. My guess is that the MOF is flexible and the movie shows no movement just for better visual inspection.
If you use a flexible framework, then all atoms should move. In MD that is done automatically; in MC you need MC-moves to do that.
Thank you for you reply and help.