Mods

platforms/brook/src/BrookGbsa.h

@@ -43,8 +43,11 @@
 namespace OpenMM {
 
 /**
- * This kernel is invoked by StandardMMForceField to calculate the forces acting on the system.
+ *
+ * Used by BrookCalcGBSAOBCForceFieldKernel kernel to execute OBC algorithm on GPU
+ *
  */
+
 class BrookGbsa : public BrookCommon {
 
    public:
@@ -309,7 +312,7 @@ class BrookGbsa : public BrookCommon {
        *
        */
       
-      int BrookGbsa::calculateBornRadii( const Stream& positions );
+      int calculateBornRadii( const Stream& positions );
       
       /* 
        * Setup of Gbsa parameters

platforms/brook/src/BrookIntegrateLangevinStepKernel.cpp

@@ -82,6 +82,8 @@ void BrookIntegrateLangevinStepKernel::initialize( const vector<double>& masses,
 
 // ---------------------------------------------------------------------------------------
    
+   _brookkStochasticDynamics = new BrookStochasticDynamics( masses );
+   _brookShakeAlgorithm      = new BrookShakeAlgorithm( masses, constraintIndices, constraintLengths );
 /*
     this->masses = new RealOpenMM[masses.size()];
     for (size_t i = 0; i < masses.size(); ++i)
@@ -131,8 +133,8 @@ void BrookIntegrateLangevinStepKernel::execute( Stream& positions, Stream& veloc
    if( _brookStochasticDynamics == NULL ){
       _brookStochasticDynamics = new BrookStochasticDynamics( getNumberOfAtoms(), static_cast<RealOpenMM>(stepSize), 
                                                               static_cast<RealOpenMM>(tau), static_cast<RealOpenMM>(temperature) );
-   } else {
-      _brookStochasticDynamics->updateParameters( temperature, friction, stepSize );
+   } else if( temperature != _brookStochasticDynamics->getTemperatur() || friction != _brookStochasticDynamics->getFriction() ){
+      _brookStochasticDynamics->updateParameters( temperature, friction );
    } 
    _brookStochasticDynamics->update( positions, velocities, forces );