{ "cells": [ { "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ "# Non-linear dimension reduction to diffusion maps\n", "\n", "Here we reduce the dimensions of a trajectory into a diffusion map.\n", "\n", "**Last updated:** December 2022 with MDAnalysis 2.4.0-dev0\n", "\n", "**Minimum version of MDAnalysis:** 0.17.0\n", "\n", "**Packages required:**\n", " \n", "* MDAnalysis (Michaud-Agrawal *et al.*, 2011, Gowers *et al.*, 2016)\n", "* MDAnalysisTests\n", "\n", "
\n", " | Mode2 | \n", "Mode3 | \n", "Mode4 | \n", "Mode5 | \n", "Mode6 | \n", "Time (ps) | \n", "
---|---|---|---|---|---|---|
0 | \n", "-0.094795 | \n", "-0.075950 | \n", "-0.054708 | \n", "-0.035526 | \n", "-0.022757 | \n", "0.0 | \n", "
1 | \n", "-0.166068 | \n", "-0.132017 | \n", "-0.094409 | \n", "-0.060914 | \n", "-0.038667 | \n", "1.0 | \n", "
2 | \n", "-0.199960 | \n", "-0.154475 | \n", "-0.107425 | \n", "-0.067632 | \n", "-0.041445 | \n", "2.0 | \n", "
3 | \n", "0.228815 | \n", "0.168694 | \n", "0.111460 | \n", "0.067112 | \n", "0.038469 | \n", "3.0 | \n", "
4 | \n", "0.250384 | \n", "0.171873 | \n", "0.103407 | \n", "0.057143 | \n", "0.028398 | \n", "4.0 | \n", "