fix import issues

Author: Meg Osato

blues/integrators.py

@@ -110,12 +110,7 @@ def __init__(self,
             measure_shadow_work=measure_shadow_work,
             measure_heat=measure_heat,
             nsteps_neq=nsteps_neq)
-
         self._prop_lambda = self._get_prop_lambda(prop_lambda)
-        frame = inspect.currentframe()
-        args, _, _, values = inspect.getargvalues(frame)
-        inputs = dict([(i, values[i]) for i in args if i is not 'self'])
-        self.int_kwargs = inputs
 
         # add some global variables relevant to the integrator
         kB = openmm.unit.BOLTZMANN_CONSTANT_kB * openmm.unit.AVOGADRO_CONSTANT_NA

blues/simulation.py

@@ -739,20 +739,12 @@ def generateSimFromStruct(cls, structure, system, integrator, platform=None, pro
 
         # Set initial positions/velocities
         if structure.box_vectors:
-            from simtk.openmm.app.internal.unitcell import reducePeriodicBoxVectors
-            from simtk.openmm.vec3 import Vec3
-            a = Vec3(*structure.box_vectors[0].value_in_unit(unit.nanometer))
-            b = Vec3(*structure.box_vectors[1].value_in_unit(unit.nanometer))
-            c = Vec3(*structure.box_vectors[2].value_in_unit(unit.nanometer))
-            old_box = [a,b,c]*unit.nanometer
-            box_vectors = reducePeriodicBoxVectors(old_box)
-
-            simulation.context.setPeriodicBoxVectors(*box_vectors)
+            simulation.context.setPeriodicBoxVectors(*structure.box_vectors)
         simulation.context.setPositions(structure.positions)
         simulation.context.setVelocitiesToTemperature(integrator.getTemperature())
 
         return simulation
-
+        
     @staticmethod
     def attachReporters(simulation, reporter_list):
         """Attach the list of reporters to the Simulation object