{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Calculating the Harmonic Ensemble Similarity between ensembles\n", "\n", "Here we compare the conformational ensembles of proteins in four trajectories, using the harmonic ensemble similarity method.\n", "\n", "**Last updated:** January 2020\n", "\n", "**Minimum version of MDAnalysis:** 0.21.0\n", "\n", "**Packages required:**\n", " \n", "* MDAnalysis (Michaud-Agrawal *et al.*, 2011, Gowers *et al.*, 2016)\n", "* MDAnalysisTests\n", "\n", "\n", "**Optional packages for visualisation:**\n", "\n", "* [matplotlib](https://matplotlib.org)\n", "\n", "\n", "