add comment/modify test

- Test system is translated to the origin
- Energy is computed again after updating Gromacs input to reflect no-cutoff option (rcoulomb = rlist = rvdw = 0.0)

wrappers/python/simtk/openmm/app/gromacstopfile.py

@@ -889,7 +889,10 @@ class GromacsTopFile(object):
                         q = float(params[4])
 
                     if has_nbfix_terms:
+                        # when NBFIX term is found, add all possible nonbond atom pairs explicitly
                         if self._defaults[1] != '2':
+                            # CHARMM parameters are compatible with the Lorentz-Berthelot combination
+                            # rule (type 2) and we will stick with that for simplicity.
                             raise NotImplemented
                         nb.addParticle(q, 1.0, 0.0)
                         atom_charges.append(q)
@@ -1053,7 +1056,10 @@ class GromacsTopFile(object):
             lj.setCutoffDistance(nonbondedCutoff)
 
         if has_nbfix_terms:
+            # when NBFIX term is found, add all possible nonbond atom pairs explicitly
             if self._defaults[1] != '2':
+                # CHARMM parameters are compatible with the Lorentz-Berthelot combination
+                # rule (type 2) and we will stick with that for simplicity.
                 raise NotImplemented
 
             atom_nbfix_types = set([])

wrappers/python/tests/TestGromacsTopFile.py

@@ -164,9 +164,10 @@ class TestGromacsTopFile(unittest.TestCase):
         context = Context(system, VerletIntegrator(1*femtosecond),
                           Platform.getPlatformByName('Reference'))
         context.setPositions(gro.positions)
+        context.computeVirtualSites()
         ene = context.getState(getEnergy=True).getPotentialEnergy()
         # the energy output is from gromacs and it only prints out 6 sig digits.
-        self.assertAlmostEqual(ene.value_in_unit(kilojoules_per_mole), 187.559, places=3)
+        self.assertAlmostEqual(ene.value_in_unit(kilojoules_per_mole), 1.88855e+02, places=3)
 
 if __name__ == '__main__':
     unittest.main()

wrappers/python/tests/systems/bnz.gro

-GROwing Monsters And Cloning Shrimps
+Gnomes, ROck Monsters And Chili Sauce
    26
-    1BEN     CG    1   4.683   2.023   2.471
-    1BEN     HG    2   4.695   2.020   2.579
-    1BEN    CD1    3   4.635   1.911   2.403
-    1BEN    HD1    4   4.611   1.821   2.457
-    1BEN    CD2    5   4.715   2.140   2.401
-    1BEN    HD2    6   4.751   2.227   2.454
-    1BEN    CE1    7   4.620   1.915   2.263
-    1BEN    HE1    8   4.583   1.828   2.210
-    1BEN    CE2    9   4.700   2.144   2.261
-    1BEN    HE2   10   4.725   2.234   2.207
-    1BEN     CZ   11   4.653   2.031   2.193
-    1BEN     HZ   12   4.642   2.035   2.086
-    1BEN    LPA   13   4.668   2.027   2.332
-    1BEN     CG   14   4.667   2.077   1.583
-    1BEN     HG   15   4.723   2.096   1.493
-    1BEN    CD1   16   4.577   1.970   1.588
-    1BEN    HD1   17   4.563   1.906   1.502
-    1BEN    CD2   18   4.683   2.160   1.695
-    1BEN    HD2   19   4.751   2.244   1.690
-    1BEN    CE1   20   4.504   1.945   1.705
-    1BEN    HE1   21   4.435   1.862   1.709
-    1BEN    CE2   22   4.612   2.134   1.813
-    1BEN    HE2   23   4.627   2.197   1.900
-    1BEN     CZ   24   4.523   2.026   1.818
-    1BEN     HZ   25   4.468   2.005   1.908
-    1BEN    LPA   26   4.595   2.052   1.700
+    1BEN     CG    1   0.052  -0.016   0.455
+    1BEN     HG    2   0.064  -0.020   0.563
+    1BEN    CD1    3   0.004  -0.129   0.386
+    1BEN    HD1    4  -0.020  -0.219   0.441
+    1BEN    CD2    5   0.084   0.100   0.385
+    1BEN    HD2    6   0.120   0.187   0.438
+    1BEN    CE1    7  -0.012  -0.125   0.247
+    1BEN    HE1    8  -0.048  -0.211   0.194
+    1BEN    CE2    9   0.069   0.104   0.245
+    1BEN    HE2   10   0.094   0.194   0.191
+    1BEN     CZ   11   0.022  -0.008   0.177
+    1BEN     HZ   12   0.011  -0.005   0.069
+    1BEN    LPA   13   0.037  -0.012   0.316
+    1BEN     CG   14   0.036   0.038  -0.433
+    1BEN     HG   15   0.092   0.057  -0.523
+    1BEN    CD1   16  -0.054  -0.070  -0.428
+    1BEN    HD1   17  -0.068  -0.133  -0.515
+    1BEN    CD2   18   0.052   0.120  -0.321
+    1BEN    HD2   19   0.120   0.205  -0.326
+    1BEN    CE1   20  -0.127  -0.095  -0.311
+    1BEN    HE1   21  -0.196  -0.178  -0.307
+    1BEN    CE2   22  -0.019   0.094  -0.203
+    1BEN    HE2   23  -0.004   0.157  -0.116
+    1BEN     CZ   24  -0.108  -0.014  -0.198
+    1BEN     HZ   25  -0.163  -0.034  -0.108
+    1BEN    LPA   26  -0.036   0.012  -0.316
    0.00000   0.00000   0.00000

wrappers/python/tests/systems/bnz.top

@@ -27,6 +27,10 @@ CG2R61    6    12.011000    0.000  A  0.355005321205  0.29288
 HGR61     1     1.008000    0.000  A  0.242003727796  0.12552
 LP        0     0.000000    0.00   A  0.0             0.0    ; pram
 
+; NBFIX for LP, rmin=1.2/2^(1/6), eps=4.184*.01
+[ nonbond_params ]
+LP     LP  1  1.069078461768  0.041840000000                 ; pram
+
 [ bondtypes ]
 ;      i        j  func           b0           kb
   CG2R61   CG2R61     1   0.13750000    255224.00
@@ -160,15 +164,6 @@ BENX              3
 ; Vsite from                    funct   a 
 13       1       11       1      0.500
 
-[ atomtypes ]
-;type atnum         mass   charge  ?           sigma  epsilon
-; special dummy-type particles
-LP      0       0.000000        0.00    A       0.0     0.0    ; pram
-
-; NBFIX for LP, rmin=1.2/2^(1/6), eps=4.184*.01
-[ nonbond_params ]
-LP     LP  1  1.069078461768  0.041840000000                 ; pram
-
 [ system ]
 ; Name
 two benzene