more changes

docs/guide/protocols/absolutesolvation.rst

@@ -5,7 +5,6 @@ Overview
 --------
 
 The :class:`absolute solvation protocol <.AbsoluteSolvationProtocol>` calculates the free energy change 
-calculates the free energy change 
 associate with transferring a molecule from vacuum into a solvent.
 
 .. note::

docs/guide/protocols/plainmd.rst

@@ -12,16 +12,23 @@ Scientific Details
 ------------------
 
 The :class:`.PlainMDProtocol` runs MD simulations of a system either in solvent or vacuum, depending on the input provided by the user in the `ChemicalSystem`.
-If there is a ``SolventComponent`` in the ``ChemicalSystem``, the protocol first performs an energy minimization of the system, 
-followed by an equilibration in the canonical ensemble as well as an equilibration in the NPT ensemble. The production run is then carried out in the NPT ensemble.
-A MonteCarloBarostat is used in the NPT ensemble to maintain constant pressure.
 The protocol applies a 
 `LangevinMiddleIntegrator <http://docs.openmm.org/development/api-python/generated/openmm.openmm.LangevinMiddleIntegrator.html>`_ 
 which uses Langevin dynamics, with the LFMiddle discretization [1]_.  
 
+Simulation Steps
+~~~~~~~~~~~~~~~~
+
+If there is a ``SolventComponent`` in the ``ChemicalSystem``, the each Protocol simulation Unit carries out the following steps:
+
+1. Parameterize the system using `OpenMMForceFields <https://github.com/openmm/openmmforcefields>`_ and `Open Force Field <https://github.com/openforcefield/openff-forcefields>`_.
+2. Minimize the system
+3. Equilibrate in the canonical ensemble
+4. Equilibrate and production simulate the system (under NPT conditions using a MonteCarloBarostat to maintain constant pressure)
+
 Relevant settings under solvent conditions include the solvation settings that control the ``solvent_model`` and ``solvent_padding``.
 
-If the ``ChemicalSystem`` does not contain a ``SolventComponent``, the protocol runs an MD simulation in vacuum. After a minimization, the protocol performs an NVT equilibration, followed by an NVT production run with no periodic boundary conditions and infinite cutoffs. Settings that control the barostat or the solvation are ignored for vaccum MD simulations
+If the ``ChemicalSystem`` does not contain a ``SolventComponent``, the protocol runs an MD simulation in vacuum. After a minimization, the protocol performs an NVT equilibration, followed by an NVT production run with no periodic boundary conditions and infinite cutoffs. Settings that control the barostat or the solvation are ignored for vaccum MD simulations.
 
 Performance consideration for gas phase MD simulations
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

docs/guide/protocols/relativehybridtopology.rst

@@ -68,6 +68,19 @@ cycle.
 This means that each :class:`.ProtocolDAG` only runs a single leg of a thermodynamic cycle and therefore two Protocol instances need to be run to get the overall relative free energy difference, DDG. 
 If multiple ``protocol_repeats`` are run (default: ``protocol_repeats=3``), the :class:`.ProtocolDAG` contains multiple units of both vacuum and solvent transformations.
 
+Simulation Steps
+~~~~~~~~~~~~~~~~
+
+Each Protocol simulation Unit carries out the following steps:
+
+1. Parameterize the system using `OpenMMForceFields <https://github.com/openmm/openmmforcefields>`_ and `Open Force Field <https://github.com/openforcefield/openff-forcefields>`_.
+2. Create an alchemical system (hybrid topology)
+3. Minimize the alchemical system
+4. Equilibrate and production simulate the alchemical system using the chosen multistate sampling method (under NPT conditions if solvent is present).
+5. Analyze results for the transformation
+
+Note: three different types of multistate sampling (i.e. replica swapping between lambda states) methods can be chosen; HREX, SAMS, and independent (no lambda swaps attempted). By default the HREX approach is selected, this can be altered using ``simulation_settings.sampler_method`` (default: ``repex``).
+
 See Also
 --------