I want to do inter-molecular cross linking using bond/create command.However, bonds are formed based on a parameter of minimum distance in bond/create.How can I ensure that bonds are not formed between atoms of same molecule (which satisfy minimum distance criteria)?
Fix bond/create is rather simple minded. It can do what is documented, if you cannot formulate your problem within the available features, then it cannot be used.
If you want more sophisticated processing, you need to look at fix bond/react.