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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]({{ site.baseurl }}/pages/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]({{ site.docs.userguide.url }}/stable/installation.html).
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:
# 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))
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To find out what else you can do, head over to [Learning MDAnalysis]({{ site.baseurl }}/learning_MDAnalysis/) to explore tutorials and documentation.
If you have questions, visit our [Community]({{ site.baseurl }}/community/) page to learn about available discussion channels. Happy coding!