Merge pull request #1349 from jchodera/fix-ionic-strength

Fix error in ionicStrength definition in Modeller.addSolvent()

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

@@ -264,7 +264,7 @@ class Modeller(object):
         2. Water molecules are removed if their distance to any solute atom is less than the sum of their van der Waals radii.
         3. If the solute is charged and neutralize=True, enough positive or negative ions are added to neutralize it.  Each ion is added by
            randomly selecting a water molecule and replacing it with the ion.
-        4. Ion pairs are added to give the requested total ionic strength.
+        4. Ion pairs are added to give the requested total ionic strength.  Note that only monovalent ions are currently supported.
 
         The box size can be specified in any of several ways:
 
@@ -298,6 +298,7 @@ class Modeller(object):
         ionicStrength : concentration=0*molar
             the total concentration of ions (both positive and negative) to add.  This
             does not include ions that are added to neutralize the system.
+            Note that only monovalent ions are currently supported.
         neutralize : bool=True
             whether to add ions to neutralize the system
         """
@@ -522,7 +523,7 @@ class Modeller(object):
         # Add ions based on the desired ionic strength.
 
         numIons = len(addedWaters)*ionicStrength/(55.4*molar) # Pure water is about 55.4 molar (depending on temperature)
-        numPairs = int(floor(numIons/2+0.5))
+        numPairs = int(floor(numIons+0.5))
         for i in range(numPairs):
             addIon(positiveElement)
         for i in range(numPairs):

wrappers/python/tests/TestModeller.py

@@ -395,7 +395,7 @@ class TestModeller(unittest.TestCase):
         total_added = water_count+sodium_count+chlorine_count
         self.assertEqual(total_added, 1364)
         expected_ion_fraction = 2.0*molar/(55.4*molar)
-        expected_ions = math.floor(total_added*expected_ion_fraction/2+0.5)
+        expected_ions = math.floor(total_added*expected_ion_fraction+0.5)
         self.assertEqual(sodium_count, expected_ions)
         self.assertEqual(chlorine_count, expected_ions)
 
@@ -437,7 +437,7 @@ class TestModeller(unittest.TestCase):
 
             total_water_ions = water_count+sodium_count+chlorine_count
             expected_ion_fraction = 1.0*molar/(55.4*molar)
-            expected_chlorine = math.floor((total_water_ions-10)*expected_ion_fraction/2+0.5)+5
+            expected_chlorine = math.floor((total_water_ions-10)*expected_ion_fraction+0.5)+5
             expected_sodium = expected_chlorine if neutralize else expected_chlorine-5
             self.assertEqual(sodium_count, expected_sodium)
             self.assertEqual(chlorine_count, expected_chlorine)
@@ -482,7 +482,7 @@ class TestModeller(unittest.TestCase):
 
             total_water_ions = water_count+sodium_count+chlorine_count
             expected_ion_fraction = 1.0*molar/(55.4*molar)
-            expected_sodium = math.floor((total_water_ions-10)*expected_ion_fraction/2+0.5)+5
+            expected_sodium = math.floor((total_water_ions-10)*expected_ion_fraction+0.5)+5
             expected_chlorine = expected_sodium if neutralize else expected_sodium-5
             self.assertEqual(sodium_count, expected_sodium)
             self.assertEqual(chlorine_count, expected_chlorine)
@@ -520,7 +520,7 @@ class TestModeller(unittest.TestCase):
 
             total_added = water_count+positive_ion_count+chlorine_count
             self.assertEqual(total_added, 1364)
-            expected_ions = math.floor(total_added*expected_ion_fraction/2+0.5)
+            expected_ions = math.floor(total_added*expected_ion_fraction+0.5)
             self.assertEqual(positive_ion_count, expected_ions)
             self.assertEqual(chlorine_count, expected_ions)
 
@@ -544,7 +544,7 @@ class TestModeller(unittest.TestCase):
 
             total_added = water_count+sodium_count+negative_ion_count
             self.assertEqual(total_added, 1364)
-            expected_ions = math.floor(total_added*expected_ion_fraction/2+0.5)
+            expected_ions = math.floor(total_added*expected_ion_fraction+0.5)
             self.assertEqual(positive_ion_count, expected_ions)
             self.assertEqual(chlorine_count, expected_ions)
 
@@ -1083,5 +1083,3 @@ class TestModeller(unittest.TestCase):
 
 if __name__ == '__main__':
     unittest.main()
-
-