Merge branch 'amoeba' of github.com:peastman/openmm

plugins/amoeba/openmmapi/include/openmm/AmoebaTorsionTorsionForce.h

@@ -126,13 +126,15 @@ public:
      * Set the torsion-torsion grid at the specified index
      *
      * @param index         the index of the torsion-torsion for which to get parameters
-     * @param grid          grid
+     * @param grid          either 3 or 6 values may be specified per grid point.  If the derivatives
+     *                      are omitted, they are calculated automatically by fitting a 2D spline to
+     *                      the energies.
      *                         grid[x][y][0] = x value
      *                         grid[x][y][1] = y value
-     *                         grid[x][y][2] = function value
-     *                         grid[x][y][3] = dfdx value
-     *                         grid[x][y][4] = dfdy value
-     *                         grid[x][y][5] = dfd(xy) value
+     *                         grid[x][y][2] = energy
+     *                         grid[x][y][3] = dEdx value
+     *                         grid[x][y][4] = dEdy value
+     *                         grid[x][y][5] = dEd(xy) value
      */
     void setTorsionTorsionGrid(int index, const std::vector<std::vector<std::vector<double> > >& grid);
 
@@ -181,29 +183,7 @@ public:
         _spacing[0]     = _spacing[1]     = 1.0;
     }
 
-    TorsionTorsionGridInfo(const TorsionTorsionGrid& grid) {
-
-        _grid.resize(grid.size());
-        for(unsigned int kk = 0; kk < grid.size(); kk++){
-            _grid[kk].resize(grid[kk].size());
-            for(unsigned int jj = 0; jj < grid[kk].size(); jj++){
-                _grid[kk][jj].resize(grid[kk][jj].size());
-                for(unsigned int ii = 0; ii < grid[kk][jj].size(); ii++){
-                    _grid[kk][jj][ii] = grid[kk][jj][ii];
-                }
-            }
-        }
-
-        _startValues[0] =  _grid[0][0][0];
-        _startValues[1] =  _grid[0][0][1];
-
-        _spacing[0]     = static_cast<double>(_grid.size()-1)/360.0;
-        _spacing[1]     = static_cast<double>(grid.size()-1)/360.0;
-
-        _size[0]        = static_cast<int>(grid.size());
-        _size[1]        = static_cast<int>(grid[0].size());
-
-    }
+    TorsionTorsionGridInfo(const TorsionTorsionGrid& grid);
 
     const TorsionTorsionGrid& getTorsionTorsionGrid(void) const {
         return _grid;

plugins/amoeba/openmmapi/src/AmoebaTorsionTorsionForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2009 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2014 Stanford University and the Authors.      *
  * Authors:                                                                   *
  * Contributors:                                                              *
  *                                                                            *
@@ -33,8 +33,10 @@
 #include "openmm/OpenMMException.h"
 #include "openmm/AmoebaTorsionTorsionForce.h"
 #include "openmm/internal/AmoebaTorsionTorsionForceImpl.h"
+#include "openmm/internal/SplineFitter.h"
 
 using namespace OpenMM;
+using namespace std;
 
 AmoebaTorsionTorsionForce::AmoebaTorsionTorsionForce() {
 }
@@ -82,3 +84,102 @@ void AmoebaTorsionTorsionForce::setTorsionTorsionGrid(int index, const TorsionTo
 ForceImpl* AmoebaTorsionTorsionForce::createImpl() const {
     return new AmoebaTorsionTorsionForceImpl(*this);
 }
+
+AmoebaTorsionTorsionForce::TorsionTorsionGridInfo::TorsionTorsionGridInfo(const TorsionTorsionGrid& grid) {
+    if (grid[0][0][0] != grid[1][0][0])
+        _grid = grid;
+    else {
+        // We need to transpose the grid.
+        
+        int xsize = grid[0].size();
+        int ysize = grid.size();
+        _grid.resize(xsize);
+        for (int i = 0; i < xsize; i++) {
+            _grid[i].resize(ysize);
+            for (int j = 0; j < ysize; j++)
+                _grid[i][j] = grid[j][i];
+        }
+    }
+
+    _startValues[0] =  _grid[0][0][0];
+    _startValues[1] =  _grid[0][0][1];
+
+    _spacing[0]     = static_cast<double>(_grid.size()-1)/360.0;
+    _spacing[1]     = static_cast<double>(_grid.size()-1)/360.0;
+
+    _size[0]        = static_cast<int>(_grid.size());
+    _size[1]        = static_cast<int>(_grid[0].size());
+    
+    if (_grid[0][0].size() == 3) {
+        // We need to compute the derivatives ourselves.  First determine if the grid is periodic.
+        
+        int xsize = _size[0];
+        int ysize = _size[1];
+        bool periodic = true;
+        for (int i = 0; i < xsize; i++)
+            if (_grid[i][0][2] != _grid[i][ysize-1][2])
+                periodic = false;
+        for (int i = 0; i < ysize; i++)
+            if (_grid[0][i][2] != _grid[xsize-1][i][2])
+                periodic = false;
+        
+        // Compute derivatives with respect to the first angle.
+
+        vector<double> x(xsize), y(ysize);
+        for (int i = 0; i < xsize; i++)
+            x[i] = _grid[i][0][0];
+        for (int i = 0; i < ysize; i++)
+            y[i] = _grid[0][i][1];
+        vector<double> d1(xsize*ysize), d2(xsize*ysize), d12(xsize*ysize);
+        vector<double> t(xsize), deriv(xsize);
+        for (int i = 0; i < ysize; i++) {
+            for (int j = 0; j < xsize; j++)
+                t[j] = _grid[j][i][2];
+            if (periodic)
+                SplineFitter::createPeriodicSpline(x, t, deriv);
+            else
+                SplineFitter::createNaturalSpline(x, t, deriv);
+            for (int j = 0; j < xsize; j++)
+                d1[j+xsize*i] = SplineFitter::evaluateSplineDerivative(x, t, deriv, x[j]);
+        }
+
+        // Compute derivatives with respect to the second angle.
+
+        t.resize(ysize);
+        deriv.resize(ysize);
+        for (int i = 0; i < xsize; i++) {
+            for (int j = 0; j < ysize; j++)
+                t[j] = _grid[i][j][2];
+            if (periodic)
+                SplineFitter::createPeriodicSpline(y, t, deriv);
+            else
+                SplineFitter::createNaturalSpline(y, t, deriv);
+            for (int j = 0; j < ysize; j++)
+                d2[i+xsize*j] = SplineFitter::evaluateSplineDerivative(y, t, deriv, y[j]);
+        }
+
+        // Compute cross derivatives.
+
+        t.resize(xsize);
+        deriv.resize(xsize);
+        for (int i = 0; i < ysize; i++) {
+            for (int j = 0; j < xsize; j++)
+                t[j] = d2[j+xsize*i];
+            if (periodic)
+                SplineFitter::createPeriodicSpline(x, t, deriv);
+            else
+                SplineFitter::createNaturalSpline(x, t, deriv);
+            for (int j = 0; j < xsize; j++)
+                d12[j+xsize*i] = SplineFitter::evaluateSplineDerivative(x, t, deriv, x[j]);
+        }
+        
+        // Add the derivatives to the grid.
+        
+        for (int i = 0; i < xsize; i++)
+            for (int j = 0; j < ysize; j++) {
+                _grid[i][j].push_back(d1[i+xsize*j]);
+                _grid[i][j].push_back(d2[i+xsize*j]);
+                _grid[i][j].push_back(d12[i+xsize*j]);
+            }
+    }
+}

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaTorsionTorsionForce.cpp

@@ -49,7 +49,7 @@ extern "C" OPENMM_EXPORT void registerAmoebaReferenceKernelFactories();
 
 const double TOL = 1e-4;
 
-TorsionTorsionGrid& getTorsionGrid( int gridIndex ) {
+TorsionTorsionGrid getTorsionGrid(int gridIndex, bool includeDerivs) {
 
 static double grid[4][625][6] = { 
     {
@@ -2557,16 +2557,14 @@ static double grid[4][625][6] = {
 {     165.0000,     180.0000, -0.182999000E+01,  0.377952854E-01,  0.233583295E-01, -0.109828932E-02 }, 
 {     180.0000,     180.0000, -0.146854000E+01,  0.491175487E-02,  0.195601580E-02, -0.163177030E-02 }  } };
 
-    // static std::vector< std::vector< std::vector<double> > > TorsionTorsionGrid
-    static std::vector<TorsionTorsionGrid> grids;
-    if( grids.size() == 0 ){
-        grids.resize(4);
+    int elementCount = (includeDerivs ? 6 : 3);
+    std::vector<TorsionTorsionGrid> grids(4);
     for( int ii = 0; ii < 4; ii++ ){
         grids[ii].resize( 25 );
         for( int jj = 0; jj < 25; jj++ ){
             grids[ii][jj].resize(25);
             for( int kk = 0; kk < 25; kk++ ){
-                    grids[ii][jj][kk].resize(6);
+                grids[ii][jj][kk].resize(elementCount);
             }
         }
         int index = 0;
@@ -2574,18 +2572,17 @@ static double grid[4][625][6] = {
             for( int kk = 0; kk < 25; kk++ ){
                 int jjIndex = static_cast<int>(((grid[ii][index][0] + 180.0)/15.0)+1.0e-05);
                 int kkIndex = static_cast<int>(((grid[ii][index][1] + 180.0)/15.0)+1.0e-05);
-                    for( int ll = 0; ll < 6; ll++ ){
+                for( int ll = 0; ll < elementCount; ll++ ){
                     grids[ii][kk][jj][ll] = grid[ii][index][ll];
                 }
                 index++;
             }
         }
     }
-    }
     return grids[gridIndex];
 }
 
-void testTorsionTorsion( FILE* log, int systemId ) {
+void testTorsionTorsion(int systemId, bool includeDerivs) {
 
     System system;
     int numberOfParticles = 6;
@@ -2645,11 +2642,11 @@ void testTorsionTorsion( FILE* log, int systemId ) {
 
         expectedEnergy        = -3.372536909E+00;
     }
-    amoebaTorsionTorsionForce->addTorsionTorsion( 0, 1, 2, 3, 4, chiralCheckAtomIndex, 0 );
-    amoebaTorsionTorsionForce->setTorsionTorsionGrid( 0, getTorsionGrid( gridIndex ) );
+    amoebaTorsionTorsionForce->addTorsionTorsion(0, 1, 2, 3, 4, chiralCheckAtomIndex, 0);
+    amoebaTorsionTorsionForce->setTorsionTorsionGrid(0, getTorsionGrid(gridIndex, includeDerivs));
     
     system.addForce(amoebaTorsionTorsionForce);
-    Context context(system, integrator, Platform::getPlatformByName( "Reference"));
+    Context context(system, integrator, Platform::getPlatformByName("Reference"));
 
     context.setPositions(positions);
     State state                      = context.getState(State::Forces | State::Energy);
@@ -2662,18 +2659,6 @@ void testTorsionTorsion( FILE* log, int systemId ) {
         forces[ii][2] *= conversion;
     }
 
-#ifdef AMOEBA_DEBUG
-    if( log ){
-        (void) fprintf( log, "computeAmoebaTorsionTorsionForces: expected energy=%14.7e %14.7e\n", expectedEnergy, state.getPotentialEnergy() );
-        for( unsigned int ii = 0; ii < forces.size(); ii++ ){
-            (void) fprintf( log, "%6u [%14.7e %14.7e %14.7e]   [%14.7e %14.7e %14.7e]\n", ii,
-                            expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2],
-                            forces[ii][0], forces[ii][1], forces[ii][2] );
-        }
-        (void) fflush( log );
-    }
-#endif
-
     double tolerance = 1.0e-03;
     for( unsigned int ii = 0; ii < forces.size(); ii++ ){
         ASSERT_EQUAL_VEC( expectedForces[ii], forces[ii], tolerance );
@@ -2687,10 +2672,8 @@ int main( int numberOfArguments, char* argv[] ) {
     try {
         std::cout << "TestReferenceAmoebaTorsionTorsionForce running test..." << std::endl;
         registerAmoebaReferenceKernelFactories();
-        //registerAmoebaCudaKernelFactories();
-
-        FILE* log = NULL;
-        testTorsionTorsion( log, 1 );
+        testTorsionTorsion(1, true);
+        testTorsionTorsion(1, false);
     } catch(const std::exception& e) {
         std::cout << "exception: " << e.what() << std::endl;
         std::cout << "FAIL - ERROR.  Test failed." << std::endl;

wrappers/python/simtk/openmm/app/data/amoeba2013.xml

 <ForceField>
  <Info>
   <Source>amoebapro13.prm</Source>
-  <DateGenerated>2014-03-11</DateGenerated>
+  <DateGenerated>2014-05-08</DateGenerated>
   <Reference>Yue Shi, Zhen Xia, Jiajing Zhang, Robert Best, Chuanjie Wu, Jay W. Ponder, and Pengyu Ren. Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins. Journal of Chemical Theory and Computation, 9(9):4046–4063, 2013.</Reference>
  </Info>
  <AtomTypes>
@@ -4273,10 +4273,1885 @@
   <TorsionTorsion class1="3" class2="1" class3="2" class4="32" class5="34" grid="1" nx="25" ny="25" />
   <TorsionTorsion class1="3" class2="1" class3="2" class4="3" class5="15" grid="2" nx="25" ny="25" />
   <TorsionTorsionGrid grid="0" nx="25" ny="25" >
+    <Grid angle1="-180.0" angle2="-180.0" f="-1.7166952" />
+    <Grid angle1="-165.0" angle2="-180.0" f="-2.83834192" />
+    <Grid angle1="-150.0" angle2="-180.0" f="-5.53476256" />
+    <Grid angle1="-135.0" angle2="-180.0" f="-9.86658328" />
+    <Grid angle1="-120.0" angle2="-180.0" f="-14.81968616" />
+    <Grid angle1="-105.0" angle2="-180.0" f="-19.85927232" />
+    <Grid angle1="-90.0" angle2="-180.0" f="-24.00000976" />
+    <Grid angle1="-75.0" angle2="-180.0" f="-26.60680912" />
+    <Grid angle1="-60.0" angle2="-180.0" f="-26.58212352" />
+    <Grid angle1="-45.0" angle2="-180.0" f="-21.98867728" />
+    <Grid angle1="-30.0" angle2="-180.0" f="-13.24846864" />
+    <Grid angle1="-15.0" angle2="-180.0" f="-4.56466032" />
+    <Grid angle1="0.0" angle2="-180.0" f="5.80684808" />
+    <Grid angle1="15.0" angle2="-180.0" f="-4.56466032" />
+    <Grid angle1="30.0" angle2="-180.0" f="-13.24846864" />
+    <Grid angle1="45.0" angle2="-180.0" f="-21.98867728" />
+    <Grid angle1="60.0" angle2="-180.0" f="-26.58212352" />
+    <Grid angle1="75.0" angle2="-180.0" f="-26.61287592" />
+    <Grid angle1="90.0" angle2="-180.0" f="-24.00000976" />
+    <Grid angle1="105.0" angle2="-180.0" f="-19.85927232" />
+    <Grid angle1="120.0" angle2="-180.0" f="-14.81968616" />
+    <Grid angle1="135.0" angle2="-180.0" f="-9.86658328" />
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+    <Grid angle1="165.0" angle2="-180.0" f="-2.83876032" />
+    <Grid angle1="180.0" angle2="-180.0" f="-1.7166952" />
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+    <Grid angle1="-165.0" angle2="-165.0" f="-3.76777568" />
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+    <Grid angle1="-135.0" angle2="-165.0" f="-11.06596872" />
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+    <Grid angle1="-105.0" angle2="-165.0" f="-20.40733448" />
+    <Grid angle1="-90.0" angle2="-165.0" f="-24.66016128" />
+    <Grid angle1="-75.0" angle2="-165.0" f="-27.44402752" />
+    <Grid angle1="-60.0" angle2="-165.0" f="-27.18558184" />
+    <Grid angle1="-45.0" angle2="-165.0" f="-21.84328328" />
+    <Grid angle1="-30.0" angle2="-165.0" f="-12.34087536" />
+    <Grid angle1="-15.0" angle2="-165.0" f="-0.35045184" />
+    <Grid angle1="0.0" angle2="-165.0" f="1.36410952" />
+    <Grid angle1="15.0" angle2="-165.0" f="-4.29479232" />
+    <Grid angle1="30.0" angle2="-165.0" f="-12.89889544" />
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+    <Grid angle1="90.0" angle2="-165.0" f="-22.01863472" />
+    <Grid angle1="105.0" angle2="-165.0" f="-17.75070368" />
+    <Grid angle1="120.0" angle2="-165.0" f="-12.59798216" />
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+    <Grid angle1="-180.0" angle2="-150.0" f="-1.44544648" />
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+    <Grid angle1="-90.0" angle2="-150.0" f="-23.39261848" />
+    <Grid angle1="-75.0" angle2="-150.0" f="-26.30263232" />
+    <Grid angle1="-60.0" angle2="-150.0" f="-20.22248536" />
+    <Grid angle1="-45.0" angle2="-150.0" f="-19.34735992" />
+    <Grid angle1="-30.0" angle2="-150.0" f="-7.63262016" />
+    <Grid angle1="-15.0" angle2="-150.0" f="5.00117704" />
+    <Grid angle1="0.0" angle2="-150.0" f="2.73077128" />
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+    <Grid angle1="90.0" angle2="-150.0" f="-18.71135008" />
+    <Grid angle1="105.0" angle2="-150.0" f="-14.38973832" />
+    <Grid angle1="120.0" angle2="-150.0" f="-9.28312448" />
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+    <Grid angle1="90.0" angle2="-120.0" f="-10.26238968" />
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+    <Grid angle1="-180.0" angle2="135.0" f="0.47936088" />
+    <Grid angle1="-165.0" angle2="135.0" f="1.6723448" />
+    <Grid angle1="-150.0" angle2="135.0" f="1.26883984" />
+    <Grid angle1="-135.0" angle2="135.0" f="-1.09491096" />
+    <Grid angle1="-120.0" angle2="135.0" f="-5.79111624" />
+    <Grid angle1="-105.0" angle2="135.0" f="-10.76639432" />
+    <Grid angle1="-90.0" angle2="135.0" f="-14.56124048" />
+    <Grid angle1="-75.0" angle2="135.0" f="-17.35297264" />
+    <Grid angle1="-60.0" angle2="135.0" f="-17.3742692" />
+    <Grid angle1="-45.0" angle2="135.0" f="-13.86970896" />
+    <Grid angle1="-30.0" angle2="135.0" f="-7.48668224" />
+    <Grid angle1="-15.0" angle2="135.0" f="-0.23551736" />
+    <Grid angle1="0.0" angle2="135.0" f="5.41447256" />
+    <Grid angle1="15.0" angle2="135.0" f="7.436014" />
+    <Grid angle1="30.0" angle2="135.0" f="4.48575008" />
+    <Grid angle1="45.0" angle2="135.0" f="-12.33095928" />
+    <Grid angle1="60.0" angle2="135.0" f="-20.72088344" />
+    <Grid angle1="75.0" angle2="135.0" f="-22.4256124" />
+    <Grid angle1="90.0" angle2="135.0" f="-19.81847832" />
+    <Grid angle1="105.0" angle2="135.0" f="-15.16507536" />
+    <Grid angle1="120.0" angle2="135.0" f="-10.09942288" />
+    <Grid angle1="135.0" angle2="135.0" f="-6.1124056" />
+    <Grid angle1="150.0" angle2="135.0" f="-3.62915976" />
+    <Grid angle1="165.0" angle2="135.0" f="-1.49649128" />
+    <Grid angle1="180.0" angle2="135.0" f="0.47936088" />
+    <Grid angle1="-180.0" angle2="150.0" f="-1.44544648" />
+    <Grid angle1="-165.0" angle2="150.0" f="-0.38379832" />
+    <Grid angle1="-150.0" angle2="150.0" f="-1.43661824" />
+    <Grid angle1="-135.0" angle2="150.0" f="-4.59352992" />
+    <Grid angle1="-120.0" angle2="150.0" f="-9.28312448" />
+    <Grid angle1="-105.0" angle2="150.0" f="-14.38973832" />
+    <Grid angle1="-90.0" angle2="150.0" f="-18.71093168" />
+    <Grid angle1="-75.0" angle2="150.0" f="-21.39563712" />
+    <Grid angle1="-60.0" angle2="150.0" f="-21.57718088" />
+    <Grid angle1="-45.0" angle2="150.0" f="-18.07496368" />
+    <Grid angle1="-30.0" angle2="150.0" f="-11.03371008" />
+    <Grid angle1="-15.0" angle2="150.0" f="-3.03938312" />
+    <Grid angle1="0.0" angle2="150.0" f="1.80861768" />
+    <Grid angle1="15.0" angle2="150.0" f="5.00075864" />
+    <Grid angle1="30.0" angle2="150.0" f="-7.63262016" />
+    <Grid angle1="45.0" angle2="150.0" f="-19.34735992" />
+    <Grid angle1="60.0" angle2="150.0" f="-25.57047416" />
+    <Grid angle1="75.0" angle2="150.0" f="-26.30263232" />
+    <Grid angle1="90.0" angle2="150.0" f="-23.39261848" />
+    <Grid angle1="105.0" angle2="150.0" f="-18.89414904" />
+    <Grid angle1="120.0" angle2="150.0" f="-14.07346976" />
+    <Grid angle1="135.0" angle2="150.0" f="-10.02164232" />
+    <Grid angle1="150.0" angle2="150.0" f="-6.74201392" />
+    <Grid angle1="165.0" angle2="150.0" f="-3.81241896" />
+    <Grid angle1="180.0" angle2="150.0" f="-1.44544648" />
+    <Grid angle1="-180.0" angle2="165.0" f="-1.73271992" />
+    <Grid angle1="-165.0" angle2="165.0" f="-1.62481456" />
+    <Grid angle1="-150.0" angle2="165.0" f="-3.5967756" />
+    <Grid angle1="-135.0" angle2="165.0" f="-7.55446304" />
+    <Grid angle1="-120.0" angle2="165.0" f="-12.59798216" />
+    <Grid angle1="-105.0" angle2="165.0" f="-17.75070368" />
+    <Grid angle1="-90.0" angle2="165.0" f="-22.01863472" />
+    <Grid angle1="-75.0" angle2="165.0" f="-24.5667744" />
+    <Grid angle1="-60.0" angle2="165.0" f="-24.64991048" />
+    <Grid angle1="-45.0" angle2="165.0" f="-20.76778608" />
+    <Grid angle1="-30.0" angle2="165.0" f="-12.89889544" />
+    <Grid angle1="-15.0" angle2="165.0" f="-4.29479232" />
+    <Grid angle1="0.0" angle2="165.0" f="1.36410952" />
+    <Grid angle1="15.0" angle2="165.0" f="-0.35045184" />
+    <Grid angle1="30.0" angle2="165.0" f="-12.34087536" />
+    <Grid angle1="45.0" angle2="165.0" f="-21.84370168" />
+    <Grid angle1="60.0" angle2="165.0" f="-27.18558184" />
+    <Grid angle1="75.0" angle2="165.0" f="-27.44402752" />
+    <Grid angle1="90.0" angle2="165.0" f="-24.66016128" />
+    <Grid angle1="105.0" angle2="165.0" f="-20.40691608" />
+    <Grid angle1="120.0" angle2="165.0" f="-15.64246976" />
+    <Grid angle1="135.0" angle2="165.0" f="-11.06638712" />
+    <Grid angle1="150.0" angle2="165.0" f="-7.05497712" />
+    <Grid angle1="165.0" angle2="165.0" f="-3.76777568" />
+    <Grid angle1="180.0" angle2="165.0" f="-1.73271992" />
+    <Grid angle1="-180.0" angle2="180.0" f="-1.7166952" />
+    <Grid angle1="-165.0" angle2="180.0" f="-2.83834192" />
+    <Grid angle1="-150.0" angle2="180.0" f="-5.53476256" />
+    <Grid angle1="-135.0" angle2="180.0" f="-9.86658328" />
+    <Grid angle1="-120.0" angle2="180.0" f="-14.81968616" />
+    <Grid angle1="-105.0" angle2="180.0" f="-19.85927232" />
+    <Grid angle1="-90.0" angle2="180.0" f="-24.00000976" />
+    <Grid angle1="-75.0" angle2="180.0" f="-26.60680912" />
+    <Grid angle1="-60.0" angle2="180.0" f="-26.58212352" />
+    <Grid angle1="-45.0" angle2="180.0" f="-21.98867728" />
+    <Grid angle1="-30.0" angle2="180.0" f="-13.24846864" />
+    <Grid angle1="-15.0" angle2="180.0" f="-4.56466032" />
+    <Grid angle1="0.0" angle2="180.0" f="5.80684808" />
+    <Grid angle1="15.0" angle2="180.0" f="-4.56466032" />
+    <Grid angle1="30.0" angle2="180.0" f="-13.24846864" />
+    <Grid angle1="45.0" angle2="180.0" f="-21.98867728" />
+    <Grid angle1="60.0" angle2="180.0" f="-26.58212352" />
+    <Grid angle1="75.0" angle2="180.0" f="-26.61287592" />
+    <Grid angle1="90.0" angle2="180.0" f="-24.00000976" />
+    <Grid angle1="105.0" angle2="180.0" f="-19.85927232" />
+    <Grid angle1="120.0" angle2="180.0" f="-14.81968616" />
+    <Grid angle1="135.0" angle2="180.0" f="-9.86658328" />
+    <Grid angle1="150.0" angle2="180.0" f="-5.53476256" />
+    <Grid angle1="165.0" angle2="180.0" f="-2.83876032" />
+    <Grid angle1="180.0" angle2="180.0" f="-1.7166952" />
 </TorsionTorsionGrid >
 </AmoebaTorsionTorsionForce>
  <AmoebaVdwForce type="BUFFERED-14-7" radiusrule="CUBIC-MEAN" radiustype="R-MIN" radiussize="DIAMETER" epsilonrule="HHG" vdw-13-scale="0.0" vdw-14-scale="1.0" vdw-15-scale="1.0" >

wrappers/python/simtk/openmm/app/data/amoeba2013_gk.xml

 <ForceField>
  <Info>
   <Source>amoebapro13.prm</Source>
-  <DateGenerated>2014-03-11</DateGenerated>
+  <DateGenerated>2014-05-08</DateGenerated>
   <Reference>Yue Shi, Zhen Xia, Jiajing Zhang, Robert Best, Chuanjie Wu, Jay W. Ponder, and Pengyu Ren. Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins. Journal of Chemical Theory and Computation, 9(9):4046–4063, 2013.</Reference>
  </Info>
  <AmoebaGeneralizedKirkwoodForce solventDielectric="78.3" soluteDielectric="1.0" includeCavityTerm="1" probeRadius="0.14" surfaceAreaFactor="-170.351730663">

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

@@ -2517,6 +2517,7 @@ class AmoebaTorsionTorsionGenerator:
                 gridRow.append(float(gridEntry.attrib['angle1']))
                 gridRow.append(float(gridEntry.attrib['angle2']))
                 gridRow.append(float(gridEntry.attrib['f']))
+                if 'fx' in gridEntry.attrib:
                     gridRow.append(float(gridEntry.attrib['fx']))
                     gridRow.append(float(gridEntry.attrib['fy']))
                     gridRow.append(float(gridEntry.attrib['fxy']))