Molecular Dynamics Simulations for Physical Chemistry Classes

Introduction

This distribution contains the following directories. Simulations are "ready to run" according to the instructions contained in this file or the documents in the Documents/ directory. Some software packages (notably the GROMACS molecular dynamics engine and the VMD visualization program) are required. Information on how to install this software is provided in the "Getting Started" section below.

• Activity1_Ideal_Real_Gases/ — MD simulation to illustrate the differences between ideal and real gases. Also introduces radial distribution functions and the connections between molecular size and interaction energy and the parameters of the van der Waals equation. This directory (and other activity directories) also contain example output and analysis.
• Activity2_Meaning_Of_Beta/ — An inquiry-based activity to uncover the meaning of the constant (beta) in the Boltzmann distribution equation from the speed distribution of a real gas.
• Activity3_Phase_Change/ — MD simulation of the compression of argon from gas to liquid, illustrating the essential features of phase transitions, the structure of the liquid state, and the calculation of energy and enthalpy of vaporization.
• Documents/ — Student notes for Activities 1 and 3, as LaTeX sources, ODT, and DOCX files. (Activity 2 is a guided inquiry, and so only has instructors' notes.)
• Prep/ — Files and scripts necessary to prepare fully-independent simulations for different students or situations. Python and the numpy and scipy libraries are required for this; the version that ships with recent version of MacOS suffices.

Each simulation directory contains an example analysis notebook. These analysis notebooks (for example Activity1_Analysis.ipynb in Activity1_Ideal_Real_Gases/) can be viewed through GitHub even without installing or running Python.

The "Getting Started" section below provides instructions for how to obtain the necessary software and use the files provided here.

Getting Started (MacOS)

The following instructions are for MacOS. Instructions for other operating systems (especially Windows) would be a welcome contribution from the community.

Installing the necessary software

The most straightforward way to get things going is to install Homebrew. Follow the (remarkably short) installation instructions as given on the Homebrew web page. Then, in the terminal, run the following:

brew install gromacs

If you wish to run the Python-based analysis notebooks, also run

brew tap homebrew/science
brew install python3 numpy scipy ipython jupyter
brew install matplotlib --with-python3

or install the Anaconda Python Distribution from https://www.anaconda.com/download/

Finally, download the VMD viewer from http://www.ks.uiuc.edu/Research/vmd/. This requires a free registration.

Downloading the files necessary to run simulations and analysis

To download the files necessary to perform the activities, clone this Git repository. Also in the terminal:

git clone https://github.com/mczwier/md_in_pchem.git

This creates a directory named md_in_pchem. This is the starting point for all of the simulations.

Running the simulations

Data files and scripts have been provided to run the simulations and extract the data necessary for further analysis. Only the software described above (GROMACS and VMD) is required. The scripts provided assume that each activity is run in sequence. This is not necessarily required from a pedagogical standpoint, but if you choose to skip an activity, you will nonetheless need to run the simulations for each prior activity before moving on. From the md_in_pchem directory created above, do the following to run the simulations for a given activity.

The first activity (ideal and real gases)

To run the simulations for the first activity, run the following commands from the terminal in the md_in_pchem directory:

cd Activity1_Ideal_Real_Gases 
./run.sh

This will take several minutes. For example, on a 2015-era MacBook Pro, this takes about five minutes. This runs the simulations and extracts energies and radial distribution functions, leaving them in the current directory (as text files ending with .xvg, which can be loaded into Excel or another analysis tool). A Finder window can be opened to interact with these files by running open . (note trailing period) in the terminal. When done with this activity, run cd .. to return to the md_in_pchem directory. Alternatively, see Act01.pdf, Act01.odt, or Act01.docx in the Documents/ directory for an equivalent step-by-step, hands-on approach.

The second activity (the meaning of thermodynamic β)

The second activity — determining the physical meaning of β in the Boltzmann distribution exp(–βE) — is an analysis-only activity, and requires the trajectories (simulations) from the first activity. Thus, if you want to use this activity, first perform the simulations for the first activity (as described above). To prepare data for analysis, execute the following, again from the md_in_pchem directory:

cd Activity2_Meaning_Of_Beta
./run.sh

This creates the files vels_100.xvg, vels_200.xvg, and vels_300.xvg, which contain the x velocities for each of the 100 argon atoms in the simulation as a function of simulation time. These files can then be loaded into your favorite analysis tool to construct histograms. For those wishing to use Excel but not wishing to use the Analysis ToolPak, a Python script (make_vel_histogram.py) has been provided to read atomic velocities and produce histograms in either a plain text table or CSV format. Python and Numpy are required, and the version of Python shipped with recent versions of MacOS suffices.

The third activity (phase changes)

The third activity — the nature of phase changes and calculation of the heat of vaporization — does not require any preparatory simulations to be performed. To run this simulation, do the following from the md_in_pchem directory:

cd Activity3_Phase_Change/
./run.sh

Alternatively, see Act03.pdf, Act03.odt, or Act03.docx in the Documents directory for step-by-step instructions for both running and analyzing the simulation.

Where to go next

Running the Jupyter analysis notebooks

If you are interested in exploring the Jupyter notebooks for analysis, install Python and the Jupyter notebook system either using Homebrew (see "Getting Started" above) or download the Anaconda Python Distribution from https://www.anaconda.com/download/. Choose the Python 3 version (not the Python 2.7 version).

Once Python is installed, run jupyter notebook from the Terminal in the md_in_pchem directory. This will start a web browser and display a listing of the contents of the md_in_pchem directory, which should include directories for each of the activities. Click on the directory for the activity whose analysis you want to run (e.g. Activity1_Ideal_Real_Gases) and click on the Jupyter notebook (extension .ipynb, e.g., Activity1_Analysis.ipynb) to start the analysis notebook. These notebooks run from top to bottom (like a Mathematica notebook, for instance); pressing Shift-Enter executes a cell and moves to the next one. To run the example analysis, just keep pressing Shift-Enter.

(Re)equilibrating the simulations

Pre-equilibrated simulations (at the correct temperature and density and every atom having an appropriate velocity) have been provided. However, to illustrate variability from simulation to simulation (or equivalently to ensure that different students have different data to work with), it is necessary to re-equilibrate (generate new velocities). This requires Python and the Numpy library (provided, for example, by the Anaconda distribution described above, or by MacOS). To re-equilibrate, execute the following prior to running simulations for each of the activities. From the md_in_pchem directory, run the following:

cd Prep
./run_equil.sh