Modified OpenMM to use nm and kJ as units instead of angstroms and kcal

openmmapi/include/GBSAOBCForceField.h

@@ -60,7 +60,7 @@ public:
      * 
      * @param index          the index of the atom for which to get parameters
      * @param charge         the charge of the atom, measured in units of the proton charge
-     * @param radius         the GBSA radius of the atom, measured in angstroms
+     * @param radius         the GBSA radius of the atom, measured in nm
      * @param scalingFactor  the OBC scaling factor for the atom
      */
     void getAtomParameters(int index, double& charge, double& radius, double& scalingFactor) const;
@@ -69,7 +69,7 @@ public:
      * 
      * @param index          the index of the atom for which to set parameters
      * @param charge         the charge of the atom, measured in units of the proton charge
-     * @param radius         the GBSA radius of the atom, measured in angstroms
+     * @param radius         the GBSA radius of the atom, measured in nm
      * @param scalingFactor  the OBC scaling factor for the atom
      */
     void setAtomParameters(int index, double charge, double radius, double scalingFactor);

openmmapi/include/OpenMMContext.h

@@ -110,14 +110,14 @@ public:
      */
     void setTime(double time);
     /**
-     * Set the positions of all atoms in the System (measured in angstroms).
+     * Set the positions of all atoms in the System (measured in nm).
      * 
      * @param a vector whose length equals the number of atoms in the System.  The i'th element
      * contains the position of the i'th atom.
      */
     void setPositions(const std::vector<Vec3>& positions);
     /**
-     * Set the velocities of all atoms in the System (measured in angstroms/picosecond).
+     * Set the velocities of all atoms in the System (measured in nm/picosecond).
      * 
      * @param a vector whose length equals the number of atoms in the System.  The i'th element
      * contains the velocity of the i'th atom.

openmmapi/include/StandardMMForceField.h

@@ -95,8 +95,8 @@ public:
      * 
      * @param index     the index of the atom for which to get parameters
      * @param charge    the charge of the atom, measured in units of the proton charge
-     * @param radius    the van der Waals radius of the atom, measured in angstroms
-     * @param depth     the well depth of the van der Waals interaction, measured in kcal/mol
+     * @param radius    the van der Waals radius of the atom, measured in nm
+     * @param depth     the well depth of the van der Waals interaction, measured in kJ/mol
      */
     void getAtomParameters(int index, double& charge, double& radius, double& depth) const;
     /**
@@ -104,8 +104,8 @@ public:
      * 
      * @param index     the index of the atom for which to set parameters
      * @param charge    the charge of the atom, measured in units of the proton charge
-     * @param radius    the van der Waals radius of the atom (sigma in the Lennard Jones potential), measured in angstroms
-     * @param depth     the well depth of the van der Waals interaction (epsilon in the Lennard Jones potential), measured in kcal/mol
+     * @param radius    the van der Waals radius of the atom (sigma in the Lennard Jones potential), measured in nm
+     * @param depth     the well depth of the van der Waals interaction (epsilon in the Lennard Jones potential), measured in kJ/mol
      */
     void setAtomParameters(int index, double charge, double radius, double depth);
     /**
@@ -114,7 +114,7 @@ public:
      * @param index     the index of the bond for which to get parameters
      * @param atom1     the index of the first atom connected by the bond
      * @param atom2     the index of the second atom connected by the bond
-     * @param length    the equilibrium length of the bond, measured in angstroms
+     * @param length    the equilibrium length of the bond, measured in nm
      * @param k         the harmonic force constant for the bond
      */
     void getBondParameters(int index, int& atom1, int& atom2, double& length, double& k) const;
@@ -124,7 +124,7 @@ public:
      * @param index     the index of the bond for which to set parameters
      * @param atom1     the index of the first atom connected by the bond
      * @param atom2     the index of the second atom connected by the bond
-     * @param length    the equilibrium length of the bond, measured in angstroms
+     * @param length    the equilibrium length of the bond, measured in nm
      * @param k         the harmonic force constant for the bond
      */
     void setBondParameters(int index, int atom1, int atom2, double length, double k);

openmmapi/include/System.h

@@ -98,7 +98,7 @@ public:
      * @param index     the index of the constraint for which to get parameters
      * @param atom1     the index of the first atom involved in the constraint
      * @param atom2     the index of the second atom involved in the constraint
-     * @param distance  the required distance between the two atoms, measured in angstroms
+     * @param distance  the required distance between the two atoms, measured in nm
      */
     void getConstraintParameters(int index, int& atom1, int& atom2, double& distance) const;
     /**
@@ -107,7 +107,7 @@ public:
      * @param index     the index of the constraint for which to set parameters
      * @param atom1     the index of the first atom involved in the constraint
      * @param atom2     the index of the second atom involved in the constraint
-     * @param distance  the required distance between the two atoms, measured in angstroms
+     * @param distance  the required distance between the two atoms, measured in nm
      */
     void setConstraintParameters(int index, int atom1, int atom2, double distance);
     /**

openmmapi/include/internal/OpenMMContextImpl.h

@@ -132,11 +132,11 @@ public:
      */
     void calcForces();
     /**
-     * Calculate the kinetic energy of the system (in kcal/mol).
+     * Calculate the kinetic energy of the system (in kJ/mol).
      */
     double calcKineticEnergy();
     /**
-     * Calculate the potential energy of the system (in kcal/mol).
+     * Calculate the potential energy of the system (in kJ/mol).
      */
     double calcPotentialEnergy();
     /**

platforms/reference/src/ReferenceKernels.cpp

@@ -231,7 +231,7 @@ void ReferenceCalcGBSAOBCForceFieldKernel::initialize(const vector<vector<double
         scaleFactors[i] = atomParameters[i][2];
     }
     ObcParameters* obcParameters  = new ObcParameters(numAtoms, ObcParameters::ObcTypeII);
-    obcParameters->setAtomicRadii(atomicRadii, SimTKOpenMMCommon::KcalAngUnits);
+    obcParameters->setAtomicRadii(atomicRadii, SimTKOpenMMCommon::MdUnits);
     obcParameters->setScaledRadiusFactors(scaleFactors);
     obcParameters->setSolventDielectric(solventDielectric);
     obcParameters->setSoluteDielectric(soluteDielectric);