Bug #533

virtual site database needs documentation

Added by Mark Abraham about 9 years ago. Updated about 9 years ago.

Target version:
Affected version - extra info:
Affected version:


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!

#2 Updated by Mark Abraham about 9 years ago

And virtual site type 4FDN needs documentation in the algorithms and topologies section of the manual, presumably partly copied from the Bjelkmar paper.

#3 Updated by Erik Lindahl about 9 years ago

vsite 4fdn documentation added, vsd stuff coming soon.

#4 Updated by Erik Lindahl about 9 years ago

.vsd file format documentation added to section 5.6 of the manual.

#5 Updated by Mark Abraham about 9 years ago

Sorry to have to raise this one again, but I don't think my comment #1 got addressed.

In subsection "Virtual sites" of topology.tex, all the examples for virtual_sites give the "Site" as "5", and it is not clear to me what significance this value has.

#6 Updated by David van der Spoel about 9 years ago

Clarified the text somewhat more but left number 5 in there. Committed in 46c5a2e.

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