{ "cells": [ { "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ "# Calculating the root mean square fluctuation over a trajectory\n", "\n", "We calculate the RMSF of the alpha-carbons in adenylate kinase (AdK) as it transitions from an open to closed structure, with reference to the average conformation of AdK.\n", "\n", "**Last updated:** December 2022 with MDAnalysis 2.4.0-dev0\n", "\n", "**Minimum version of MDAnalysis:** 1.0.0\n", "\n", "**Packages required:**\n", " \n", "* MDAnalysis (Michaud-Agrawal *et al.*, 2011, Gowers *et al.*, 2016)\n", "* [MDAnalysisData](https://www.mdanalysis.org/MDAnalysisData/)\n", "* [matplotlib](https://matplotlib.org/)\n", "* [nglview](http://nglviewer.org/nglview/latest/)\n", "\n", "**See also**\n", "\n", "* [RMSD](rmsd.ipynb)\n", "* [Pairwise (2D) RMSD](pairwise_rmsd.ipynb)\n", "\n", "