We will use some computer software to perform calculations and visualize some of our results. All this software is available for Windows, Mac OS X, and Linux operating systems, and available free of charge for academic users. Please go ahead and install the following on your computer.
- Visual Molecular Dynamics
A fantastic program to visualize molecular structures and Molecular Dynamics trajectories.
- IPython / SciPy / Matplotlib
Python is a fun and easy-to-learn programming language, and together with Scipy and Matplotlib provides a wonderful environment for scientific computations. There are many different ways to obtain these programs; here are a few suggestions:
- If you are using Linux, chances are that all these programs are available in your distribution's software repository.
- If you are using Mac OS X, you can use the MacPorts package manager to install a myriad of free software packages. After downloading MacPorts, you should be able to install all the required software by entering
sudo port install py27-ipython py27-scipy py27-matplotlib
in a terminal window. If this is the first time you are using MacPorts, this will take many hours to complete.
- Whether you use Windows, OS X, or Linux, you can download the Enthought Python Distribution, which is free for academic use.
If you are interested in learning how to program in Python, here are two great resources:
- The Python Tutorial is an easy to follow overview of the the main features if this programming language.
- The Python Scientific Lecture Notes also provide an overview of the Python basics, and also include a discussion of main libraries used for numerical computations.
Please let me know if you are having difficulties obtaining and installing these programs.