MDAnalysis is a Python library for analyzing molecular dynamics (MD) simulations. This page will guide you through quickly installing MDAnalysis, exploring a basic example, and accessing learning resources to get started.
Our Installation Quick Start guide contains instructions to get MDAnalysis up and running in a few minutes. Try this guide first.
For a more thorough installation with advanced options, including dependencies and environment configurations, see the installation instructions in the User Guide.
Once MDAnalysis is installed, you can load a trajectory and perform a simple analysis. A typical usage pattern is to iterate through a trajectory and analyze coordinates for every frame.
In the following example, the end-to-end distance of a protein and the radius of gyration of the backbone atoms are calculated:
import MDAnalysis
from MDAnalysis.tests.datafiles import PSF, DCD # test trajectory
import numpy.linalg
# load trajectory and topology into a Universe
u = MDAnalysis.Universe(PSF,DCD)
# from the 4AKE segid, select
# the first atom named N and the last atom named C
nterm = u.select_atoms('segid 4AKE and name N')[0]
cterm = u.select_atoms('segid 4AKE and name C')[-1]
# select the backbone atoms (AtomGroup)
bb = u.select_atoms('protein and backbone')
for ts in u.trajectory: # iterate through all frames
r = cterm.position - nterm.position # end-to-end vector from atom positions
d = numpy.linalg.norm(r) # end-to-end distance
rgyr = bb.radius_of_gyration() # method of AtomGroup
print("frame = {0}: d = {1} A, Rgyr = {2} A".format(
ts.frame, d, rgyr))
To find out what else you can do, head over to Learning MDAnalysis to explore tutorials and documentation.
If you have questions, visit our Community page to learn about available discussion channels. Happy coding!