

In [ ]:

    
from __future__ import print_function
import numpy as np
import mdtraj as md
np.set_printoptions(threshold=50)

Sometimes your molecular dynamics trajectory files are too large to fit into memory. This can make analysis a burden, because you have to be very aware of the size of various objects. This can be a challenge in python because of the language's automatic memory management.

Fortunately, python provides the iterator protocol that can help us out here. We can "stream through" a trajectory, without loading the entire thing into memory at all. Instead, we'll process it in chunks.

For the purpose of this example, we'll use a short trajectory that's included with MDTraj for testing purposes. When you use this recipe yourself, you probably will want to point your code to your own trajectory file



In [ ]:

    
import mdtraj.testing
traj_filename = mdtraj.testing.get_fn('frame0.h5')

First, if you only want a single frame of a trajectory, there's no reason to load up the whole thing. md.load_frame can load up a single frame for you. Let's get the first one.



In [ ]:

    
first_frame = md.load_frame(traj_filename, 0)
first_frame

Using md.iterload, you can iterate through chunks of the trajectory. If you don't retain a reference to the chunk as you iterate through, then the python garbage collector can recycle the memory.



In [ ]:

    
rmsds = []
for chunk in md.iterload(traj_filename, chunk=100):
    rmsds.append(md.rmsd(chunk, first_frame))
    print(chunk, '\n', chunk.time)

Now, we've calculated all of the rmsds chunk by chunk, and we can take a look at them.



In [ ]:

    
rmsds = np.concatenate(rmsds)

print(rmsds)
print('max rmsd ', np.max(rmsds), 'at index', np.argmax(rmsds))



In [ ]: