Run some dynamics to improve the minimized structure

pdbfixer.py

@@ -394,6 +394,8 @@ class PDBFixer(object):
             context = mm.Context(system, integrator)
             context.setPositions(newPositions)
             mm.LocalEnergyMinimizer.minimize(context)
+            integrator.step(1000)
+            mm.LocalEnergyMinimizer.minimize(context)
             state = context.getState(getPositions=True)
             
             # Now create a new Topology, including all atoms from the original one and adding the missing atoms.