Merge pull request #530 from swails/longrange

Update default long-range option and expand test

wrappers/python/simtk/openmm/app/internal/amber_file_parser.py

@@ -889,6 +889,7 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
         if nonbondedMethod in ('PME', 'Ewald', 'CutoffPeriodic'):
             cforce.setNonbondedMethod(cforce.CutoffPeriodic)
             cforce.setCutoffDistance(nonbondedCutoff)
+            cforce.setUseLongRangeCorrection(True)
         elif nonbondedMethod == 'CutoffNonPeriodic':
             cforce.setNonbondedMethod(cforce.CutoffNonPeriodic)
             cforce.setCutoffDistance(nonbondedCutoff)

wrappers/python/tests/TestAmberPrmtopFile.py

@@ -145,8 +145,38 @@ class TestAmberPrmtopFile(unittest.TestCase):
         totalMass2 = sum([system2.getParticleMass(i) for i in range(system2.getNumParticles())]).value_in_unit(amu)
         self.assertAlmostEqual(totalMass1, totalMass2)
 
-    def test_NBFIX(self):
-        """Test that prmtop files with modified off-diagonal LJ elements are treated properly"""
+#   def test_NBFIX_LongRange(self):
+#       """Test prmtop files with NBFIX LJ modifications w/ long-range correction"""
+#       system = prmtop3.createSystem(nonbondedMethod=PME,
+#                                     nonbondedCutoff=8*angstroms)
+#       # Check the forces
+#       has_nonbond_force = has_custom_nonbond_force = False
+#       nonbond_exceptions = custom_nonbond_exclusions = 0
+#       for force in system.getForces():
+#           if isinstance(force, NonbondedForce):
+#               has_nonbond_force = True
+#               nonbond_exceptions = force.getNumExceptions()
+#           elif isinstance(force, CustomNonbondedForce):
+#               has_custom_nonbond_force = True
+#               custom_nonbond_exceptions = force.getNumExclusions()
+#       self.assertTrue(has_nonbond_force)
+#       self.assertTrue(has_custom_nonbond_force)
+#       self.assertEqual(nonbond_exceptions, custom_nonbond_exceptions)
+#       integrator = VerletIntegrator(1.0*femtoseconds)
+#       # Use reference platform, since it should always be present and
+#       # 'working', and the system is plenty small so this won't be too slow
+#       sim = Simulation(prmtop3.topology, system, integrator, Platform.getPlatformByName('Reference'))
+#       # Check that the energy is about what we expect it to be
+#       sim.context.setPeriodicBoxVectors(*inpcrd3.boxVectors)
+#       sim.context.setPositions(inpcrd3.positions)
+#       ene = sim.context.getState(getEnergy=True, enforcePeriodicBox=True).getPotentialEnergy()
+#       ene = ene.value_in_unit(kilocalories_per_mole)
+#       # Make sure the energy is relatively close to the value we get with
+#       # Amber using this force field.
+#       self.assertAlmostEqual(-7099.44989739/ene, 1, places=3)
+
+    def test_NBFIX_noLongRange(self):
+        """Test prmtop files with NBFIX LJ modifications w/out long-range correction"""
         system = prmtop3.createSystem(nonbondedMethod=PME,
                                       nonbondedCutoff=8*angstroms)
         # Check the forces
@@ -159,6 +189,7 @@ class TestAmberPrmtopFile(unittest.TestCase):
             elif isinstance(force, CustomNonbondedForce):
                 has_custom_nonbond_force = True
                 custom_nonbond_exceptions = force.getNumExclusions()
+                force.setUseLongRangeCorrection(False)
         self.assertTrue(has_nonbond_force)
         self.assertTrue(has_custom_nonbond_force)
         self.assertEqual(nonbond_exceptions, custom_nonbond_exceptions)