Number of monovalent ions added is now correctly determined from ionic strength.

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):