use UpdatePositions function of simulation object instead of manually setting the positions

examples/code_fragments/mm/ethanol_example.py

@@ -22,9 +22,7 @@ class Anim(QtCore.QTimer):
         
     def OnTimer(self):
         self.sim.Steps(1)
-        positions = sim.GetPositions()
-        for a, pos in zip(self.ent.atoms,positions):
-          self.ed.SetAtomPos(a,pos)
+        self.sim.UpdatePositions()
         self.go.UpdatePositions()
 
 

examples/code_fragments/mm/ethanol_example_using_topology.py

@@ -36,9 +36,7 @@ class Anim(QtCore.QTimer):
           self.counter += 1
 
         self.sim.Steps(1)
-        positions = sim.GetPositions()
-        for a, pos in zip(self.ent.atoms,positions):
-          self.ed.SetAtomPos(a,pos)
+        self.sim.UpdatePositions()
         self.go.UpdatePositions()
         self.steps+=1
 

examples/code_fragments/mm/gb_example.py

@@ -22,10 +22,7 @@ class Anim(QtCore.QTimer):
         
     def OnTimer(self):
         self.sim.Steps(5)
-        positions = sim.GetPositions()
-        for a, pos in zip(self.ent.atoms,positions):
-          self.ed.SetAtomPos(a,pos)
-        self.ed.UpdateICS()
+        self.sim.UpdatePositions()
         self.go.UpdatePositions()