added a test for nbfix generator

wrappers/python/tests/TestForceField.py

@@ -11,6 +11,7 @@ try:
 except ImportError:
     from io import StringIO
 import os
+import warnings
 
 class TestForceField(unittest.TestCase):
     """Test the ForceField.createSystem() method."""
@@ -535,6 +536,66 @@ class AmoebaTestForceField(unittest.TestCase):
             diff = norm(f1-f2)
             self.assertTrue(diff < 0.1 or diff/norm(f1) < 1e-3)
 
+    def test_nbfix_generator(self):
+        """ Test the nbfix generator"""
+        warnings.filterwarnings('ignore', category=CharmmPSFWarning)
+        psf = CharmmPsfFile('systems/ions.psf')
+        pdb = PDBFile('systems/ions.pdb')
+        params = CharmmParameterSet('systems/toppar_water_ions.str')
+
+        # Box dimensions (found from bounding box)
+        psf.setBox(12.009*angstroms,   12.338*angstroms,   11.510*angstroms)
+
+        # Turn off charges so we only test the Lennard-Jones energies
+        for a in psf.atom_list:
+            a.charge = 0.0
+
+        # Now compute the full energy
+        plat = Platform.getPlatformByName('Reference')
+        system = psf.createSystem(params, nonbondedMethod=PME,
+                                  nonbondedCutoff=5*angstroms)
+
+        con = Context(system, VerletIntegrator(2*femtoseconds), plat)
+        con.setPositions(pdb.positions)
+
+        # Now set up stystem from ffxml. Setting chareges to 0 so we only test the Lennard-Jones energies
+        xml = """
+<ForceField>
+ <AtomTypes>
+  <Type name="SOD" class="SOD" element="Na" mass="22.98977"/>
+  <Type name="CLA" class="CLA" element="Cl" mass="35.45"/>
+ </AtomTypes>
+ <Residues>
+  <Residue name="CLA">
+   <Atom name="CLA" type="CLA" charge="0"/>
+  </Residue>
+  <Residue name="SOD">
+   <Atom name="SOD" type="SOD" charge="0"/>
+  </Residue>
+ </Residues>
+ <NonbondedForce coulomb14scale="1.0" lj14scale="1.0">
+  <UseAttributeFromResidue name="charge"/>
+  <Atom type="SOD" sigma="0.251367073323" epsilon="0.1962296"/>
+  <Atom type="CLA" sigma="0.404468018036" epsilon="0.6276"/>
+ </NonbondedForce>
+ <NBFixForce>
+  <NBFix type1="CLA" type2="SOD" emin="0.350933" rmin="0.3731"/>
+ </NBFixForce>
+</ForceField> """
+
+        ff = ForceField(StringIO(xml))
+        system2 = ff.createSystem(pdb.topology, nonbondedMethod=PME,
+                                  nonbondedCutoff=5*angstroms)
+        con2 = Context(system2, VerletIntegrator(2*femtoseconds), plat)
+        con2.setPositions(pdb.positions)
+
+        state = con.getState(getEnergy=True, enforcePeriodicBox=True)
+        ene = state.getPotentialEnergy().value_in_unit(kilocalories_per_mole)
+        state2 = con2.getState(getEnergy=True, enforcePeriodicBox=True)
+        ene2 = state2.getPotentialEnergy().value_in_unit(kilocalories_per_mole)
+        self.assertAlmostEqual(ene, ene2)
+
+
     def test_Wildcard(self):
         """Test that PeriodicTorsionForces using wildcard ('') for atom types / classes in the ffxml are correctly registered"""
 

wrappers/python/tests/systems/ions.pdb

+CRYST1   12.009   12.338   11.510  90.00  90.00  90.00 P 1
+ATOM      1  SOD SOD I   1      -5.844   1.432   3.239  1.00  0.00      ION NA
+ATOM      2  CLA CLA I   2      -5.605  -3.153   1.213  1.00  0.00      ION CL
+END
\ No newline at end of file

wrappers/python/tests/systems/ions.psf

+PSF
+
+       4 !NTITLE
+ REMARKS original generated structure x-plor psf file
+ REMARKS topology ../../../../../Charmm36_FF/toppar/top_all36_cgenff.rtf 
+ REMARKS topology ../../../../../Charmm36_FF/toppar/toppar_water_ions.str 
+ REMARKS segment ION { first NONE; last NONE; auto angles dihedrals }
+
+       2 !NATOM
+       1 ION  1    SOD  SOD  SOD    1.000000       22.9898           0
+       2 ION  2    CLA  CLA  CLA   -1.000000       35.4500           0
+
+       0 !NBOND: bonds
+
+
+       0 !NTHETA: angles
+
+
+       0 !NPHI: dihedrals
+
+
+       0 !NIMPHI: impropers
+
+
+       0 !NDON: donors
+
+
+       0 !NACC: acceptors
+
+
+       0 !NNB
+
+       0       0
+
+       1       0 !NGRP
+       0       0       0
+