The Python and Bash source code in this work are public domain and can be reused without any restrictions.
The texts and images in the Jupyter notebooks, Markdown documents and other files are licensed under the Creative Commons Attribution 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.
This tutorial shows how to use and install different software packages, which have their own conditions of use.
This tutorial was written for the course Molecular Simulations of Biological Systems (MSBS), a (very) introductory course for students of the MSc program Biochemistry and Biotechnology at Ghent University. The main goal of the course is to enable these students (who have a limited background in statistical mechanics) to run sensible molecular dynamics simulations and to interpret the results correctly. This tutorial assumes the students have a basic knowledge of Python.
All material strongly inspired by several online resources (tutorials, documentation and examples) of the OpenMM, Python, NumPy, Matplotlib and other projects. The main pointers are:
- OpenMM website: http://openmm.org/
- OpenMM Users Guide: http://docs.openmm.org/latest/userguide/index.html
- OpenMM script builder: http://builder.openmm.org
- Python website: https://www.python.org/
- Python tutorial: https://docs.python.org/3/tutorial/index.html
- NumPy website: https://numpy.org/
- NumPy Users Guid: https://docs.scipy.org/doc/numpy/user/index.html
- MatPlotLib website: https://matplotlib.org/
- nglview: http://nglviewer.org/nglview/latest/
- MDTraj: http://mdtraj.org/1.9.3/
- CHARMM-GUI: http://www.charmm-gui.org/
Even though these resources contain all the background and details to learn OpenMM and related tools, the amount of information is simply overwhelming. The aim of this course is to provide a gentle introduction to many of the topics in the above references.
Practically all simulations in this tutorial are carried with OpenMM, which is described in extenso here. In short, OpenMM is a modern open-source biomolecular simulation toolkit: it supports many popular biomolecular force fields (AMBER, CHARMM, AMOEBA), it supports GPU-accelerated calculations and it can carry out many types of advanced molecular dynamics simulations.
To access and customize all these features, and to write reproducible simulation protocols, OpenMM simulations are implemented by writing Python scripts. Hence, to install OpenMM, you need (to create) a Python environment and install OpenMM as a Python package. (The C++ interfaces is not covered in this tutorial.)
For this tutorial, three environments can be used to perform simulations, each having there strengths and weaknesses. It is recommended to follow this tutorial by running Jupyter notebooks on your own laptop, as explained below. Google Colab can be used as a fallback in case the installation of OpenMM on your laptop failed. In section 3 of the tutorial, it is discussed how to transfer a notebook from your laptop to Google Colab or to an HPC environment (and back).
Strengths:
- Calculations require no network.
- Output files are stored locally.
- Easy visualization in the notebook with nglview.
- You can work interactively.
Weaknesses:
- The installation requires some work.
- Your laptop could overheat when running longer simulations.
- Yout laptop must remain powered on during calculations.
Installation instructions: setup_on_your_laptop.md
Strengths:
- Requires no software installation on your laptop, other than a web browser.
- GPU acceleration can speed up calculations.
- You can work interactively.
Weaknesses:
- Your laptop must remain powered on during the calculations and your network connection cannot drop. Especially when connected through Eduroam, this can be challenging.
- Output files are deleted after closing your notebook session.
- Transferring files from and to your laptop is tedious and slow.
- A Google account required.
- Trajectories cannot be visualized inside a notebook because nglview is not supported.
Installation Instructions: setup_on_google_colab.md
Strengths:
- Calculations run in the background on a remote machine. You can power off your laptop while they run.
- You have access to more computational power.
Weaknesses:
- Some Linux knowledge is required.
- Your calculations do not start instantly. Instead, you submit "jobs" which are executed when a compute node becomes available.
Installation instructions: setup_on_a_hpc.md
This section assumes you have just installed OpenMM, following the instructions of the previous section.
To start any notebook from the tutorial, download the ZIP file with the most recent notebooks and unzip this archive.
-
On Windows open a Conda prompt and change the directory to where you unzipped the archive. If needed, first change to the correct drive, e.g. by typing the command
D:, then use e.g.cdfolowed by the name of the directory where the ZIP file was unpacked. -
On MacOS or Linux, open any terminal emulator and change the directory to where you unzipped the archive. There is no need to change drives and the usage of
cdis similar to Windows.
Then enter the following commands:
conda activate openmm
jupyter notebookA browser window should pop up in which you can select and open a notebook. If you are not familiar with notebooks, the following resources can be helpful: Jupyter Notebook Introduction.
Instructions for these environments are part of the tutorial below, see
directory 03_elsewhere.
The getting-started instructions showed you how to open a new notebook or to start any notebook from this tutorial. The tutorial consists of the following sections, to be followed more-or-less in order:
1. First steps:
2. Different ways of simulating analine dipeptide:
3. Running OpenMM notebooks in other places:
4. A short protein MD simulation:
5. Analysis of MD trajectories:
- 05_analysis/01_internal_coordinates_averages.ipynb
- 05_analysis/02_physicochemical_properties.ipynb
- 05_analysis/03_alignment_principal_component_analysis.ipynb
6. Visalization
7. Ligands
A list of common problems is compiled here: FAQ.md