Getting Started in Computational Chemistry: Glossary

Key Points

  • The basic workflow of most computational chemistry research is setting up input files for calculations or simulations, running those calculations, retrieving the output, and processing and analyzing the results.

The Terminal
  • The bash shell is one of the most common terminal applications and is frequently used to run computational chemistry software.

Text Editors
  • Many different text editors are available.

  • Some text editors are command line only (used from the terminal) while others have graphical user interfaces.

  • Many people prefer to use a modern text editor most of the time, but it is important to learn to use a command line text editor in case it is the only option available.

Using Remote Computing Resources
  • The ssh protocol is used to access remote computing resources.

  • The scp protocol is used to transfer files between computers.

  • Most remote computing resources will have a job manager to manage the submission and running of calculations. Using a job manager requires creating a submission script for your job in addition to the input file for the actual program.

Using Anaconda to Install Software
  • Anaconda can be used to install many Python-based software packages at one time.

Jupyter Notebooks
  • A Jupyter notebook is a python interpreter that lets you combine text, code, and images in one file.