virtual site database needs documentation
I think the .vsd files now in the force fields might need a section in the databases section of the topologies chapter of the manual.
#1 Updated by Mark Abraham about 9 years ago
While we're there, all the examples for [ virtual_sites? ] use the value "5" for the "Site" parameter before the list of constructing atom indexes. Is that the index of the virtual site? If so, why does this interaction have an index and not the others? (i.e. should it have an index?)
I ask because I think this should be clear to the reader of section 5.2.2 of the git manual. I'm happy to make it so, but I don't yet have the understanding to do so!