Revert "Add mrdna.simulate.multiresolution_simulation(...,center_object =...

Revert "Add mrdna.simulate.multiresolution_simulation(...,center_object = True,...) to center objects at each step during multiresolution simulations, avoiding drift to locations where PDB format cannot be used"

This reverts commit 0fdd92dc.

bin/mrdna

@@ -132,9 +132,7 @@ def main():
     if args.dimensions is None:
         dim = [max(x,1000) for x in model.dimensions_from_structure( padding_factor=2.5 )]
         model.dimensions = dim
-        # model.origin = model.get_center()-0.5*np.array(model.dimensions)
-        model.translate( -model.get_center() )
-        model.origin = -0.5*np.array(model.dimensions)
+        model.origin = model.get_center()-0.5*np.array(model.dimensions)
     else:
         model.dimensions = args.dimensions
 
@@ -196,7 +194,6 @@ def main():
             oxdna_output_period = args.oxdna_output_period,
             enrg_md_steps = args.enrg_md_steps,
             write_pqr = args.write_pqr,
-            center_object = args.dimensions is None,
             run_enrg_md = args.run_enrg_md
         )
 

mrdna/simulate.py

@@ -92,7 +92,6 @@ def multiresolution_simulation( model, output_name,
                                 write_pqr = False,
                                 run_enrg_md = False,
                                 enrg_md_steps = 1e6,
-                                center_object = True,
                                 arbd = None
                             ):
 
@@ -141,8 +140,6 @@ def multiresolution_simulation( model, output_name,
                     coordinates = readArbdCoords('%s.0.restart' % full_output_prefix)
                     
             model.update_splines(coordinates)
-            if center_object:
-                model.translate( -model.get_center() )
             simulation_step += 1
 
         coarse_model_args = dict( max_basepairs_per_bead = 5,
@@ -153,8 +150,6 @@ def multiresolution_simulation( model, output_name,
         # TODO: add the output directory in to the readArbdCoords functions or make it an attribute of the model object 
 
         """ Prepare coarse model for minimization and coarse simulation """
-        if center_object:
-            model.translate( -model.get_center() )
         model.clear_beads()
         model.generate_bead_model( **coarse_model_args )