Merge pull request #1594 from peastman/friction

Fixed friction coefficient in explicit solvent benchmarks

examples/benchmark.py

@@ -63,11 +63,13 @@ def runOneTest(testName, options):
             else:
                 method = app.CutoffPeriodic
                 cutoff = 1*unit.nanometers
+            friction = 1*(1/unit.picoseconds)
         else:
             ff = app.ForceField('amber99sb.xml', 'amber99_obc.xml')
             pdb = app.PDBFile('5dfr_minimized.pdb')
             method = app.CutoffNonPeriodic
             cutoff = 2*unit.nanometers
+            friction = 91*(1/unit.picoseconds)
         if options.heavy:
             dt = 0.005*unit.picoseconds
             constraints = app.AllBonds
@@ -77,7 +79,7 @@ def runOneTest(testName, options):
             constraints = app.HBonds
             hydrogenMass = None
         system = ff.createSystem(pdb.topology, nonbondedMethod=method, nonbondedCutoff=cutoff, constraints=constraints, hydrogenMass=hydrogenMass)
-        integ = mm.LangevinIntegrator(300*unit.kelvin, 91*(1/unit.picoseconds), dt)
+        integ = mm.LangevinIntegrator(300*unit.kelvin, friction, dt)
     print('Step Size: %g fs' % dt.value_in_unit(unit.femtoseconds))
     properties = {}
     initialSteps = 5