In the following we are using ipython as our interactive Python interpreter. It has a number of very useful features:
use the interactive help (command? or command??)
TAB completion, e.g. MDAnalysis.U<TAB> will autocomplete to MDAnalysis.Universe.
MDAnalysis.Universe.<TAB> will show all methods and attributes.
quick plotting with matplotlib (and array manipulations with numpy)
notebook mode (future versions of this tutorial will likely be provided as ipython notebooks): ipython notebook --matplotlib=inline
Start ipython:
ipython --matplotlib
Inside ipython, load numpy
import numpy as np
as we will constantly make use of its capabilities.
MDAnalysis is primarily a library that provides means to work with particle-based simulation trajectories (including single frames such as PDB files). As such, it is mainly used
In both cases, we always import the module MDAnalysis at the top level:
import MDAnalysis
(Not all sub-modules are imported automatically; for instance, analysis modules such as MDAnalysis.analysis.rms have to be imported explicitly.)
MDAnalysis comes with a bunch of test files and trajectories. One is a trajectory of the enzyme adenylate kinase that samples a transition from a closed to an open conformation [Beckstein2009], which we will use as an example throughout the tutorial. The topology file (CHARMM PSF format) and trajectory (CHARMM DCD format) can be loaded into the variables PSF and DCD:
from MDAnalysis.tests.datafiles import PSF, DCD