adapt FEP tests to not trigger GROMACS exclusion/rlist limitation

- close #175
- use better error handling in runMD_or_exit to check if we triggered the
  non-bonded interactions beyond cutoff issue and if so, pass with xfail

mdpow/tests/test_fep_script.py

@@ -1,8 +1,9 @@
-from . import tempdir as td
-
 import os
+import pytest
 import pybol
 
+from . import tempdir as td
+
 import gromacs
 
 import mdpow
@@ -43,14 +44,26 @@ def _run_fep(self, solvent, dirname):
             gromacs.cbook.edit_mdp(mdp,
                                    new_mdp=os.path.join(os.getcwd(), fep_mdp_name),
                                    cutoff_scheme="group")
-        self.S = fep_simulation(cfg, solvent, dirname=dirname)
+        self.savefilename = fep_simulation(cfg, solvent, dirname=dirname, exit_on_error=False)
 
-    def test_default_run(self):
+    def test_default_run(self, capsys):
         with gromacs.utilities.in_dir(self.tmpdir.name, create=False):
             try:
                 self._run_fep('water', 'benzene/')
             except Exception as err:
-                raise AssertionError('FEP simulations failed with exception:\n{0}'.format(str(err)))
+                # check if log file contains
+                #   'There are 2 perturbed non-bonded pair interactions beyond the pair-list cutoff'
+                # This error can happen and still counts as passing. (It is stochastic and is due
+                # to a poorly designed test system together with GROMACS having become better at detecting
+                # internal problems.)
+                captured = capsys.readouterr()
+                for line in captured:
+                    if "perturbed non-bonded pair interactions beyond the pair-list cutoff'" in line:
+                        pytest.xfail("Stochastic test failure (perturbed non-bonded beyond cutoff). "
+                                     "Still works as expected, see #175.")
+                        break
+                else:
+                    raise AssertionError('FEP simulations failed with exception:\n{0}'.format(str(err)))
 
             assert os.path.exists(os.path.join(self.tmpdir.name,
                                                'benzene', 'FEP', 'water', 'VDW', '0000', 'md.edr'))