Hi Jacopo,
For the case you have described you have to manually activate Geant4-DNA at runtime / in a macro file so that it is only applied to a certain region. You can do this with the command “/process/em/AddDNARegion <PHYSICAL_VOLUME_NAME> DNA_Opt0”. EM Standard Physics only will be invoked in all other regions.
If calling this command leads to an error re: “illegal application state” see my post here.
Joseph