Added description of enhanced sampling methods to manual

docs-source/usersguide/application.rst

@@ -1101,16 +1101,6 @@ algorithm\ :cite:`Tuckerman1992`.  This allows some forces in the system to be e
 frequently than others.  For details on how to use it, consult the API
 documentation.
 
-aMD Integrator
---------------
-
-There are three different integrator types that implement variations of the
-aMD\ :cite:`Hamelberg2007` accelerated sampling algorithm: :class:`AMDIntegrator`,
-:class:`AMDForceGroupIntegrator`, and :class:`DualAMDIntegrator`.  They
-perform integration on a modified potential energy surface to allow much faster
-sampling of conformations.  For details on how to use them, consult the API
-documentation.
-
 Compound Integrator
 -------------------
 
@@ -1371,6 +1361,55 @@ a checkpoint file every 5,000 steps, for example:
 
 Note that the checkpoint reporter will overwrite the last checkpoint file.
 
+
+Enhanced Sampling Methods
+=========================
+
+In many situations, the goal of a simulation is to sample the range of configurations
+accessible to a system.  It does not matter whether the simulation represents a
+single, physically realistic trajectory, only whether it produces a correct distribution
+of states.  In this case, a variety of methods can be used to sample configuration
+space much more quickly and efficiently than a single physical trajectory would.
+These are known as enhanced sampling methods.  OpenMM offers several that you
+can choose from.  They are briefly described here.  Consult the API documentation
+for more detailed descriptions and example code.
+
+Simulated Tempering
+-------------------
+
+Simulated tempering\ :cite:`Marinari1992` involves making frequent changes to the
+temperature of a simulation.  At high temperatures, it can quickly cross energy barriers
+and explore a wide range of configurations.  At lower temperatures, it more thoroughly
+explores each local region of configuration space.  This is a powerful method to
+speed up sampling when you do not know in advance what motions you want to sample.
+Simply specify the range of temperatures to simulate and the algorithm handles
+everything for you mostly automatically.
+
+Metadynamics
+------------
+
+Metadynamics\ :cite:`Barducci2008` is used when you do know in advance what
+motions you want to sample.  You specify one or more collective variables, and the
+algorithm adds a biasing potential to make the simulation explore a wide range of
+values for those variables.  It does this by periodically adding "bumps" to the biasing
+potential at the current values of the collective variables.  This encourages the simulation
+to move away from regions it has already explored and sample a wide range of values.
+At the end of the simulation, the biasing potential can be used to calculate the
+free energy of the system as a function of the collective variables.
+
+Accelerated Molecular Dynamics (aMD)
+------------------------------------
+
+aMD\ :cite:`Hamelberg2007` is another method that can be used when you do not know in
+advance what motions you want to accelerate.  It alters the potential energy surface
+by adding a "boost" potential whenever the potential energy is below a threshold.
+This makes local minima shallower and allows more frequent transitions between them.
+The boost can be applied to the total potential energy, to just a subset of interactions
+(typically the dihedral torsions), or both.  There are separate integrator classes
+for each of these options: :class:`AMDIntegrator`, :class:`AMDForceGroupIntegrator`,
+and :class:`DualAMDIntegrator`.
+
+
 .. _model-building-and-editing:
 
 Model Building and Editing

docs-source/usersguide/references.bib

@@ -29,6 +29,18 @@
    type = {Journal Article}
 }
 
+@article{Barducci2008,
+  title = {Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method},
+  author = {Barducci, Alessandro and Bussi, Giovanni and Parrinello, Michele},
+  journal = {Physical Review Letters},
+  volume = {100},
+  issue = {2},
+  pages = {020603},
+  year = {2008},
+  publisher = {American Physical Society},
+  doi = {10.1103/PhysRevLett.100.020603},
+}
+
 @article{Berendsen1987
    author = {Berendsen, H. J. C. and Grigera, J. R. and Straatsma, T. P.},
    title = {The missing term in effective pair potentials},
@@ -290,6 +302,18 @@
    type = {Journal Article}
 }
 
+@article{Marinari1992,
+    doi = {10.1209/0295-5075/19/6/002},
+    year = 1992,
+    publisher = {{IOP} Publishing},
+    volume = {19},
+    number = {6},
+    pages = {451--458},
+    author = {E Marinari and G Parisi},
+    title = {Simulated Tempering: A New Monte Carlo Scheme},
+    journal = {Europhysics Letters ({EPL})},
+}
+
 @article{Markland2008
    author = {Markland, Thomas E. and Manolopoulos, David E.},
    title = {An efficient ring polymer contraction scheme for imaginary time path integral simulations},