Merge pull request #3826 from peastman/vsite

Added a link to the manual section describing vsite types

docs-source/usersguide/application/05_creating_ffs.rst

@@ -172,7 +172,8 @@ Each :code:`<VirtualSite>` tag indicates an atom in the residue that should
 be represented with a virtual site.  The :code:`type` attribute may equal
 :code:`"average2"`\ , :code:`"average3"`\ , :code:`"outOfPlane"`\ , or
 :code:`"localCoords"`\ , which correspond to the TwoParticleAverageSite, ThreeParticleAverageSite,
-OutOfPlaneSite, and LocalCoordinatesSite classes respectively.  The :code:`siteName`
+OutOfPlaneSite, and LocalCoordinatesSite classes respectively.  See Section
+:numref:`virtual-sites` for descriptions of how the virtual site classes work.  The :code:`siteName`
 attribute gives the name of the atom to represent with a virtual site.  The atoms
 it is calculated based on are specified by :code:`atomName1`\ , :code:`atomName2`\ , etc.
 (Some old force fields use the deprecated tags :code:`index`, :code:`atom1`,

docs-source/usersguide/theory/05_other_features.rst

@@ -116,6 +116,8 @@ call :code:`setIntegrationForceGroups()` on the :class:`Integrator`.  Any groups
 omitted will be ignored during simulation, but can be queried at any time by
 calling :code:`getState()`.
 
+.. _virtual-sites:
+
 Virtual Sites
 *************