Added documentation on the switching and fixed the yaml page pointers
@@ -215,6 +215,28 @@ See the ``yank script`` command line docs for more information on the ``-o`` fla
.. note:: The ``CPU`` platform will automatically use all available cores/hyperthreads in serial mode, but in MPI mode, will use a single thread to avoid causing problems in queue-regulated parallel systems. To control the number of threads yourself, set the ``OPENMM_NUM_THREADS`` environment variable to the desired number of threads.
+Breaking up Simulations
+=======================
+
+One limitation simulations run to compute free energy is that you need sufficient data to estimate all legs of the
+:ref:`thermodynamic cycle <yank_cycle>` before you can estimate many properties. YANK by default simulates each phase of
+the thermodynamic cycle sequentially, meaning you have to wait for simulation completion before you can do any kind of
+analysis.
+
+YANK allows its simulations to switch between phases of the thermodynamic cycle mid-simulation. Setting the
+:ref:`yaml_options_switch_phase_interval` option in the YAML file allows you to control how many iterations the
+simulation will run of one phase before switching to the other to allow collection between each phase on-the-fly, and
+therefore allowing analysis at any point. This feature is helpful for those who want to run for an arbitrarily long
+length of time, then wish to end the simulation after some convergence criteria is met, e.g. error in free energy
+estimate.
+
+YANK also provides a way flip between different experiments when setting the
+:ref:`\!Combinatorial <yaml_combinatorial_head>` flag. The :ref:`yaml_options_switch_experiment_interval` allows
+simulations to cycle through all the experiments created when users invoke the ``!Combinatorial`` flag. This option
+can be set in tandem with the :ref:`yaml_options_switch_phase_interval`. Please see the respective documentation on
+these options for more information.
+
+..
Extending Simulations
=====================
