[WIP] fix for writing of virtuals in Desmond #304
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See comments in individual commits. A WIP for solution to issue #297. Mostly working, 1) but the energies are not quite right for several virtual tests, 2) TIP4P crashes, I think because of exclusions issues, and 3) exceptions need to be added for virtual geometries that don't work (or in some cases, canonicalizing functions need to be called).