<jupyter_start><jupyter_text>Importing Libraries<jupyter_code>import os
import mdtraj as md
import seaborn as sns
import matplotlib.pyplot as plt
import nglview as nv<jupyter_output>/home/diego/Myusr/opt/miniconda3/envs/UIBCDFLab_dev/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  return f(*args, **kwds)
/home/diego/Myusr/opt/miniconda3/envs/UIBCDFLab_dev/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  return f(*args, **kwds)
/home/diego/Myusr/opt/miniconda3/envs/UIBCDFLab_dev/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  return f(*args, **kwds)
/home/diego/Myusr/opt/miniconda3/envs/UIBCDFLab_dev/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  return f(*args, **kwds)
/home/diego/Myusr/opt/miniconda3/envs/UIBCDFLab_dev/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning: numpy.dty[...]<jupyter_text>Initial original CG traj<jupyter_code>def adding_path(file_name):    
    #return os.path.join('/home/diego/Projects/MOP_CG/elnedynp',file_name)
    return os.path.join('/home/diego/Trabajo/Proyectos/MOP_CG/elnedynp',file_name)

pdb_file  = adding_path('cell.pdb')
traj_file = adding_path('cell.xtc')
top_file  = adding_path('topol.tpr')<jupyter_output><empty_output><jupyter_text>Test tng piece of trajectory with whole system (200 frames)<jupyter_code>traj_chunks_iterator = md.iterload(traj_file, top=pdb_file, chunk=200)
first_200_frames = next(traj_chunks_iterator)
first_200_frames.save('MOP_whole_200.tng')
del(traj_chunks_iterator, first_200_frames)<jupyter_output><empty_output><jupyter_text>At this point `MOP_whole_200.tng` is stored together with the a copy of the original pdb `cell.pdb` renamed as `MOP_whole.pdb` in the directory `Examples/Data/MOP/CG`  Test h5 piece of trajectory only with MOP (10000 frames)<jupyter_code>first_frame = md.load(traj_file, top=pdb_file, frame=0)
beads_protein_indices = first_frame.topology.select('protein')
mop_traj = md.load(traj_file, top=pdb_file, atom_indices=beads_protein_indices)
mop_traj.slice(range(10000)).save('MOP.h5')<jupyter_output>/home/diego/Myusr/opt/miniconda3/envs/UIBCDFLab_dev/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  return f(*args, **kwds)
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