fix for scaled 1-4 LJ interactions when NBFIX is present in Gromacs topology file (#5032)

* fix to correctly read Gromacs topology files for CHARMM force field

* updated fix to correctly read topology files with NBFIX and different combination rules

* fixes to read topology files with NBFIX and different combination rules

* changed default for useDispersionCorrection to True

* changed docstring default for useDispersionCorrection to 'True'

* fix scaling of 1-4 LJ pairs when NBFIX is used

wrappers/python/openmm/app/gromacstopfile.py

@@ -1158,7 +1158,7 @@ class GromacsTopFile(object):
                 eps4 = float(params4[7])
 
                 charge_prod = fudgeQQ*q1*q4
-                epsilon = math.sqrt(abs(eps1 * eps4))
+                epsilon = math.sqrt(abs(eps1 * eps4))*fudgeLJ
                 if self._defaults[1] == '2':
                     rmin14 = (rmin1 + rmin4) / 2
                 else:

wrappers/python/tests/TestGromacsTopFile.py

@@ -257,7 +257,8 @@ class TestGromacsTopFile(unittest.TestCase):
            'apgr.nonbfix.pairs.comb3.top': -993.104,
            'apgr.nonbfix.nopairs.comb1.top': -918.572,
            'apgr.nonbfix.nopairs.comb2.top': -909.637,
-           'apgr.nonbfix.nopairs.comb3.top': -918.572
+           'apgr.nonbfix.nopairs.comb3.top': -918.572,
+           'apgr.nbfix.nopairs.comb2.fudge.top': -856.721
         }
         
         for topfile, expected in energies.items():