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User Guide for MDAnalysis (GSoD Project)
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MDAnalysis User Guide

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MDAnalysis is a Python toolkit to analyze molecular dynamics trajectories generated by a wide range of popular simulation packages including DL_Poly, CHARMM, Amber, NAMD, LAMMPS, and Gromacs. (See the lists of supported trajectory formats and topology formats.)

import MDAnalysis as mda

# Load simulation results with a single line
u = mda.Universe('topol.tpr','traj.trr')

# Select atoms
ag = u.select_atoms('name OH')

# Atom data made available as Numpy arrays

# Iterate through trajectories
for ts in u.trajectory:

There are also a number of tutorials on the MDAnalysis homepage that explain how to conduct RMSD calculations, Alignment and more features of MDAnalysis.

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