Dear APSDft,
The .gro file is missing but I guess you want to build a non-orthorhombic surface by Au and Pt which are frozen to keep the surface. In your decription the freeze does not work, resulting in the surface deformation. There is a similar topic in the forum which might help you (https://gromacs.bioexcel.eu/t/help-with-freeze-groups-in-gromacs-holding-a-surface-fixed-in-space/4934/2)
Therefore, using gmx make_ndx to make a .ndx file including the all Au and Pt and use this .ndx to specify the freeze group with energy group exclusions maybe could solve the problem. Additionally, if this also doesn’t work, I think use position_restraints in .top file to fix atoms would also be a resonable method.