Enable grompp to read virtual_site1

Enable grompp to read virtual_site1

In !306, a virtual site with one constructing atom was introduced.
grompp was, however, not updated to understand the new topology entry.
This updates the topology format in grompp and the manual. It also adds
a missing example for virtual site type 2fd to the manual.

Found while investigating #3866, but not directly connected.