Added documentation to clarify behavior of nonbonded exceptions (#3470)

* Added documentation to clarify behavior of nonbonded exceptions

* Added documentation to clarify behavior of nonbonded exceptions

docs-source/usersguide/theory/02_standard_forces.rst

@@ -236,6 +236,12 @@ where :math:`r_\mathit{cutoff}` is the cutoff distance and :math:`\epsilon_\math
 the dielectric constant of the solvent.  In the limit :math:`\epsilon_\mathit{solvent}` >> 1,
 this causes the force to go to zero at the cutoff.
 
+The reaction field approximation is not applied to nonbonded exceptions.  They
+are always evaluated at full strength, regardless of the cutoff distance.  That
+is because exceptions are primarily used to model 1-4 interactions, which are
+really a type of bonded interaction.  They are typically parametrized without a
+cutoff together with the other bonded interactions.
+
 Coulomb Interaction With Ewald Summation
 ========================================
 

openmmapi/include/openmm/NonbondedForce.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2021 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2022 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -353,6 +353,10 @@ public:
      * Add an interaction to the list of exceptions that should be calculated differently from other interactions.
      * If chargeProd and epsilon are both equal to 0, this will cause the interaction to be completely omitted from
      * force and energy calculations.
+     * 
+     * Regardless of the NonbondedMethod used by this Force, cutoffs are never applied to exceptions.  That is because
+     * they are primarily used for 1-4 interactions, which are really a type of bonded interaction and are parametrized
+     * together with the other bonded interactions.
      *
      * In many cases, you can use createExceptionsFromBonds() rather than adding each exception explicitly.
      *
@@ -381,6 +385,10 @@ public:
      * Set the force field parameters for an interaction that should be calculated differently from others.
      * If chargeProd and epsilon are both equal to 0, this will cause the interaction to be completely omitted from
      * force and energy calculations.
+     * 
+     * Regardless of the NonbondedMethod used by this Force, cutoffs are never applied to exceptions.  That is because
+     * they are primarily used for 1-4 interactions, which are really a type of bonded interaction and are parametrized
+     * together with the other bonded interactions.
      *
      * @param index      the index of the interaction for which to get parameters
      * @param particle1  the index of the first particle involved in the interaction