Restraint forces

docs/releasehistory.rst

@@ -3,6 +3,8 @@ Release History
 
 Development snapshot
 ====================
+- Add radially-symmetric restraint custom forces (`#336 <https://github.com/choderalab/openmmtools/pull/336>`_).
+- Copy Python attributes of integrators on ``deepcopy()`` (`#336 <https://github.com/choderalab/openmmtools/pull/336>`_).
 
 
 0.14.0 - Exact treatment of alchemical PME electrostatics, water cluster test system, optimizations

openmmtools/alchemy.py

@@ -391,6 +391,7 @@ def __setstate__(self, serialization):
         """Set the state from a dictionary representation."""
         parameters = serialization['parameters']
         alchemical_variables = serialization['alchemical_variables']
+        # New attribute in OpenMMTools 0.14.0.
         update_alchemical_charges = serialization.get('update_alchemical_charges', True)
         alchemical_functions = dict()
 

openmmtools/cache.py

@@ -489,7 +489,7 @@ def _standardize_integrator(cls, integrator):
 
         """
         standard_integrator = copy.deepcopy(integrator)
-        integrators.RestorableIntegrator.restore_interface(standard_integrator)
+        integrators.ThermostatedIntegrator.restore_interface(standard_integrator)
         for attribute, std_value in cls.COMPATIBLE_INTEGRATOR_ATTRIBUTES.items():
             try:  # setter
                 getattr(standard_integrator, 'set' + attribute)(std_value)

openmmtools/constants.py

@@ -6,3 +6,7 @@
 # (openmm/platforms/reference/include/SimTKOpenMMRealType.h)
 # TODO: Replace this with an import from simtk.openmm.constants once available
 ONE_4PI_EPS0 = 138.935456
+
+# Standard-state volume for a single molecule in a box of size (1 L) / (avogadros number).
+LITER = 1000.0 * u.centimeters**3
+STANDARD_STATE_VOLUME = LITER / (u.AVOGADRO_CONSTANT_NA*u.mole)

openmmtools/forcefactories.py

@@ -69,7 +69,7 @@ def replace_reaction_field(reference_system, switch_width=1.0*unit.angstrom,
         force_constructor = getattr(forces, 'UnshiftedReactionFieldForce')
 
     # Add an reaction field for each CutoffPeriodic NonbondedForce.
-    for reference_force in forces.iterate_nonbonded_forces(system):
+    for reference_force in forces.find_forces(system, openmm.NonbondedForce).values():
         if reference_force.getNonbondedMethod() == openmm.NonbondedForce.CutoffPeriodic:
             reaction_field_force = force_constructor.from_nonbonded_force(reference_force, switch_width=switch_width)
             system.addForce(reaction_field_force)