{"cells": [{"cell_type": "markdown", "metadata": {}, "source": ["# Exercise: Molecular Dynamics Analysis"]}, {"cell_type": "markdown", "metadata": {}, "source": ["In this exercise we will work on simulation data for the *solution NMR structure of a small peptide* (PDB-ID 6a5j). Refer to the last exercise for details on the preparation of the simulation. You can download the trajectory file `simulation.dcd` (~150 ns total length, 20 ps time step) [here](md_analysis/simulation.dcd). A topology of the simulated system can be constructed from `simulation.pdb`, available [here](md_analysis/simulation.pdb).\n", "\n", "