I'm implementing a TOP file reader, and I have a question about an ambiguity in the format. The [ pairs ] block lists atom pairs that should be handled specially (exclusions and 1-4 interactions). In addition, the gen-pairs flag can indicate that pairs are generated automatically. But all the files I've looked at include BOTH of these things, and I'm not sure how to interpret that.
Can I assume that all pairs generated by gen-pairs are already included in the list, or might I have to generate additional ones? Can I assume that all pairs listed in the file where generated by gen-pairs, or might there be additional pairs that came from somewhere else? What if the two definitions disagree with each other, and the [ pairs ] block lists different parameters for a pair than would be generated automatically? Which should I use? Thanks. Peter-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
