The Domain Similarity Matrix (DSM) is similar to amino acid substitution matrices but for domains. However, its values are not computed from alignments of domain arrangements but by aligning the HMMs of two domains using hhsearch from the hhsuite.
We have a set of precomputed matrices for different databases (see end of the page for older versions):
The domain similarity matrix will need to be copied into the “dsm” subfolder of your domain world folder. Have a look here. It will then be enough to provide the matrix by name (e.g. pfam-31.dsm) to the program and it will automatically know where to look for the file.