On this site, these terms apply to software, data and other materials that are available for download.
An associated publication either announced the availability of a download or necessitated a download. For example, it might be a publication describing a program available for download or a publication explaining a class of force fields for which we provide downloads. That is, it is a publication directly tied to the download in some manner.
A related publication provides supporting information for the download. For example, it might be a paper that explains the theoretical background behind a program.