allow to generate simulation without attaching an integrator to

the settings object.

In many cases the user might only want to minimize a structure,
an integrator is therefore useless. To make OpenMM happy, a
dummy integrator (Verlet integrator with timestep 1fs) is
attached to the settings object and simulation in these cases.

modules/mol/mm/src/simulation.cc

@@ -253,10 +253,13 @@ void Simulation::Init(const TopologyPtr top,
 
 
   top_ = top;
-  integrator_ = settings->integrator;
-  if(!integrator_){
-    throw ost::Error("Settings must have a valid integrator attached to set up a simulation!");
+
+  if(!settings->integrator){
+    //user did not specify an integrator, so let's just use a standard integrator
+    settings->integrator = IntegratorPtr(new OpenMM::VerletIntegrator(0.001));
   }
+  integrator_ = settings->integrator;
+
   system_ = SystemCreator::Create(top_,settings,system_force_mapper_); 
 
   //setting up the context, which combines the system with an integrator

modules/mol/mm/tests/test_simulation.cc

@@ -42,9 +42,6 @@ BOOST_AUTO_TEST_CASE(test_simulation_basics){
   top->AddHarmonicPositionRestraint(1,geom::Vec3(0.0,0.0,0.0),10.0);
   top->AddHarmonicDistanceRestraint(1,2,10.0,10.0);
 
-  //try to set up simulation without an integrator
-  BOOST_CHECK_THROW(Simulation sim(test_ent,settings),ost::Error);
-
   settings->integrator = IntegratorPtr(new OpenMM::VerletIntegrator(0.002));
 
   Simulation sim(top, test_ent, settings);