Improved Doxygen comments to mention updateParametersInContext().

openmmapi/include/openmm/CustomAngleForce.h

@@ -51,6 +51,7 @@ namespace OpenMM {
  * parameters, and addGlobalParameter() to define global parameters.  The values of per-angle parameters are specified as
  * part of the system definition, while values of global parameters may be modified during a simulation by calling Context::setParameter().
  * Finally, call addAngle() once for each angle.  After an angle has been added, you can modify its parameters by calling setAngleParameters().
+ * This will have no effect on Contexts that already exist unless you call updateParametersInContext().
  *
  * As an example, the following code creates a CustomAngleForce that implements a harmonic potential:
  *

openmmapi/include/openmm/CustomBondForce.h

@@ -51,6 +51,7 @@ namespace OpenMM {
  * parameters, and addGlobalParameter() to define global parameters.  The values of per-bond parameters are specified as
  * part of the system definition, while values of global parameters may be modified during a simulation by calling Context::setParameter().
  * Finally, call addBond() once for each bond.  After a bond has been added, you can modify its parameters by calling setBondParameters().
+ * This will have no effect on Contexts that already exist unless you call updateParametersInContext().
  *
  * As an example, the following code creates a CustomBondForce that implements a harmonic potential:
  *

openmmapi/include/openmm/CustomCompoundBondForce.h

@@ -69,7 +69,8 @@ namespace OpenMM {
  * Context::setParameter().
  *
  * Next, call addBond() to define bonds and specify their parameter values.  After a bond has been added, you can
- * modify its parameters by calling setBondParameters().
+ * modify its parameters by calling setBondParameters().  This will have no effect on Contexts that already exist unless
+ * you call updateParametersInContext().
  *
  * As an example, the following code creates a CustomCompoundBondForce that implements a Urey-Bradley potential.  This
  * is an interaction between three particles that depends on the angle formed by p1-p2-p3, and on the distance between

openmmapi/include/openmm/CustomExternalForce.h

@@ -50,7 +50,8 @@ namespace OpenMM {
  * parameters, and addGlobalParameter() to define global parameters.  The values of per-particle parameters are specified as
  * part of the system definition, while values of global parameters may be modified during a simulation by calling Context::setParameter().
  * Finally, call addParticle() once for each particle that should be affected by the force.  After a particle has been added,
- * you can modify its parameters by calling setParticleParameters().
+ * you can modify its parameters by calling setParticleParameters().  This will have no effect on Contexts that already exist unless
+ * you call updateParametersInContext().
  *
  * As an example, the following code creates a CustomExternalForce that attracts each particle to a target position (x0, y0, z0)
  * via a harmonic potential:

openmmapi/include/openmm/CustomGBForce.h

@@ -119,9 +119,10 @@ namespace OpenMM {
  * After defining the force as shown above, you should then call addParticle() once for each particle in the System to set the
  * values of its per-particle parameters (q, radius, and scale).  The number of particles for which you set parameters must be
  * exactly equal to the number of particles in the System, or else an exception will be thrown when you try to create a Context.
- * After a particle has been added, you can modify its parameters by calling setParticleParameters().
+ * After a particle has been added, you can modify its parameters by calling setParticleParameters().  This will have no effect
+ * on Contexts that already exist unless you call updateParametersInContext().
  *
- * CustomNonbondedForce also lets you specify "exclusions", particular pairs of particles whose interactions should be
+ * CustomGBForce also lets you specify "exclusions", particular pairs of particles whose interactions should be
  * omitted from calculations.  This is most often used for particles that are bonded to each other.  Even if you specify exclusions,
  * however, you can use the computation type ParticlePairNoExclusions to indicate that exclusions should not be applied to a
  * particular piece of the computation.

openmmapi/include/openmm/CustomHbondForce.h

@@ -68,7 +68,7 @@ namespace OpenMM {
  *
  * Next, call addDonor() and addAcceptor() to define donors and acceptors and specify their parameter values.
  * After a donor or acceptor has been added, you can modify its parameters by calling setDonorParameters() or
- * setAcceptorParameters().
+ * setAcceptorParameters().  This will have no effect on Contexts that already exist unless you call updateParametersInContext().
  *
  * CustomHbondForce also lets you specify "exclusions", particular combinations of donors and acceptors whose
  * interactions should be omitted from force and energy calculations.  This is most often used for particles

openmmapi/include/openmm/CustomNonbondedForce.h

@@ -57,7 +57,8 @@ namespace OpenMM {
  * Next, call addParticle() once for each particle in the System to set the values of its per-particle parameters.
  * The number of particles for which you set parameters must be exactly equal to the number of particles in the
  * System, or else an exception will be thrown when you try to create a Context.  After a particle has been added,
- * you can modify its parameters by calling setParticleParameters().
+ * you can modify its parameters by calling setParticleParameters().  This will have no effect on Contexts that already exist
+ * unless you call updateParametersInContext().
  *
  * CustomNonbondedForce also lets you specify "exclusions", particular pairs of particles whose interactions should be
  * omitted from force and energy calculations.  This is most often used for particles that are bonded to each other.

openmmapi/include/openmm/CustomTorsionForce.h

@@ -51,6 +51,7 @@ namespace OpenMM {
  * parameters, and addGlobalParameter() to define global parameters.  The values of per-torsion parameters are specified as
  * part of the system definition, while values of global parameters may be modified during a simulation by calling Context::setParameter().
  * Finally, call addTorsion() once for each torsion.  After an torsion has been added, you can modify its parameters by calling setTorsionParameters().
+ * This will have no effect on Contexts that already exist unless you call updateParametersInContext().
  *
  * As an example, the following code creates a CustomTorsionForce that implements a harmonic potential:
  *

openmmapi/include/openmm/GBSAOBCForce.h

@@ -45,7 +45,8 @@ namespace OpenMM {
  * System to define its parameters.  The number of particles for which you define GBSA parameters must
  * be exactly equal to the number of particles in the System, or else an exception will be thrown when you
  * try to create a Context.  After a particle has been added, you can modify its force field parameters
- * by calling setParticleParameters().
+ * by calling setParticleParameters().  This will have no effect on Contexts that already exist unless you
+ * call updateParametersInContext().
  */
 
 class OPENMM_EXPORT GBSAOBCForce : public Force {

openmmapi/include/openmm/HarmonicAngleForce.h

@@ -43,7 +43,8 @@ namespace OpenMM {
 /**
  * This class implements an interaction between groups of three particles that varies harmonically with the angle
  * between them.  To use it, create a HarmonicAngleForce object then call addAngle() once for each angle.  After
- * an angle has been added, you can modify its force field parameters by calling setAngleParameters().
+ * an angle has been added, you can modify its force field parameters by calling setAngleParameters().  This will
+ * have no effect on Contexts that already exist unless you call updateParametersInContext().
  */
 
 class OPENMM_EXPORT HarmonicAngleForce : public Force {

openmmapi/include/openmm/HarmonicBondForce.h

@@ -43,7 +43,8 @@ namespace OpenMM {
 /**
  * This class implements an interaction between pairs of particles that varies harmonically with the distance
  * between them.  To use it, create a HarmonicBondForce object then call addBond() once for each bond.  After
- * a bond has been added, you can modify its force field parameters by calling setBondParameters().
+ * a bond has been added, you can modify its force field parameters by calling setBondParameters().  This will
+ * have no effect on Contexts that already exist unless you call updateParametersInContext().
  */
 
 class OPENMM_EXPORT HarmonicBondForce : public Force {

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) 2008-2010 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -53,7 +53,8 @@ namespace OpenMM {
  * System to define its parameters.  The number of particles for which you define nonbonded parameters must
  * be exactly equal to the number of particles in the System, or else an exception will be thrown when you
  * try to create a Context.  After a particle has been added, you can modify its force field parameters
- * by calling setParticleParameters().
+ * by calling setParticleParameters().  This will have no effect on Contexts that already exist unless you
+ * call updateParametersInContext().
  *
  * NonbondedForce also lets you specify "exceptions", particular pairs of particles whose interactions should be
  * computed based on different parameters than those defined for the individual particles.  This can be used to

openmmapi/include/openmm/PeriodicTorsionForce.h

@@ -43,7 +43,8 @@ namespace OpenMM {
 /**
  * This class implements an interaction between groups of four particles that varies periodically with the torsion angle
  * between them.  To use it, create a PeriodicTorsionForce object then call addTorsion() once for each torsion.  After
- * a torsion has been added, you can modify its force field parameters by calling setTorsionParameters().
+ * a torsion has been added, you can modify its force field parameters by calling setTorsionParameters().  This will
+ * have no effect on Contexts that already exist unless you call updateParametersInContext().
  */
 
 class OPENMM_EXPORT PeriodicTorsionForce : public Force {

openmmapi/include/openmm/RBTorsionForce.h

@@ -44,6 +44,7 @@ namespace OpenMM {
  * This class implements an interaction between groups of four particles that varies with the torsion angle between them
  * according to the Ryckaert-Bellemans potential.  To use it, create an RBTorsionForce object then call addTorsion() once
  * for each torsion.  After a torsion has been added, you can modify its force field parameters by calling setTorsionParameters().
+ * This will have no effect on Contexts that already exist unless you call updateParametersInContext().
  */
 
 class OPENMM_EXPORT RBTorsionForce : public Force {