Tutorial

In this short tutorial, we’ll walk you through a basic example using enspara to make an MSM and do a simple analysis.

• Clustering Trajectories
• Fitting
• Analysis

Before you get started, however, let’s download some molecular dynamics data! This MD data is of the Fs peptide (Ace-A_5(AAARA)_3A-NME), which is a fairly common model system for studying protein folding. It was prepared by Robert McGibbon for MSMBuilder3.

mkdir fs_peptide && cd fs_peptide
wget https://ndownloader.figshare.com/articles/1030363/versions/1 -O fs_peptide.zip
unzip fs_peptide.zip

While you’re waiting for that download, check the textbook on MSMs, “An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation” edited by Greg Bowman, Vijay Pande, and Frank Noe. That book describes the theoretical and empirical groundwork for a lot of what we’ll do.

Anyway, once your download is finished, if you ls, you should see a bunch of trajectories (*.xtc), a pdb file fs-peptide.pdb, and a few other files. If you do, you’re ready to move on.