Creating a gold slab in Gromacs

GROMACS version:
GROMACS modification: Yes/No
Here post your question I want to understand the functionalization of gold slab with 3MPA to use it for biosensor applications. I am not able to create a topology file for gold slab as it deletes all the duplicate atoms. My topology file in the end has only 1 atom. How can I resolve this? I am relatively new to gromacs. Thanks


The zero valent gold atoms will have a single atom in topology file. The gro/pdb file will have coordinates for all the gold atoms in the slab. Note that if you have any ligands or functional groups attached, those will have to be added separately in the topology file.