Personal commit to make modeller easier to use

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

@@ -734,7 +734,6 @@ class Modeller(object):
                                     else:
                                         delta = Vec3(random.random(), random.random(), random.random())*nanometer
                                     delta *= 0.1*nanometer/norm(delta)
-                                    if len(expected) > 1:
                                     delta += 0.05*Vec3(random.random(), random.random(), random.random())*nanometer
                                     delta *= 0.1*nanometer/norm(delta)
                                     newPositions.append(self.positions[parent.index]+delta)
@@ -758,7 +757,9 @@ class Modeller(object):
             if atoms[i].element != elem.hydrogen:
                 # This is a heavy atom, so make it immobile.
                 system.setParticleMass(i, 0)
-        context = Context(system, VerletIntegrator(0.0))
+        from simtk.openmm import Platform
+        plt = Platform.getPlatformByName('Reference')
+        context = Context(system, VerletIntegrator(0.0), plt)
         context.setPositions(newPositions)
         LocalEnergyMinimizer.minimize(context)
         self.topology = newTopology