What is Software?

What is Computational Chemistry?

This list focuses on free software that is useful to chemistry students and teachers.

Chemistry Software

Structure drawing


Accelrys Draw


Small molecule visualization


TINKER - Software Tools for Molecular Design

Crystallographic Database Free Software: Mercury

Free Alternative to Gaussview: Avogadro

Macromolecule visualization





Electronic structure







GaussSum: Software for processing output; especially useful for density of states plots from Gaussian calculations. See the GaussSum installation for mac below in the Macports section and see
for the tar file. This page also has the all-in-one installer for Windows.

Molecular dynamics






Solid State Structures

Atomic Simulation Environment or ASE
See instructions below for install ASE via Macports and pip.

Data Visualization

  • The free, scriptable Gnuplot software is capable of creating presentation-grade quality output, as can be seen at the blog Gnuplot Tricks or, more concisely, at the web page Impossible gnuplot graphs. See the gnu plot commands in the Macports list below.
  • A popular alternative is xmgrace. See the xmgr/grace commands in the Macports list below.
  • The Dislin package by the German Max-Planck-Gesellschaft is a graphical library for scientific data presentation that can be called from a variety of programming environments, including perl scripts, and is free for non-commercial use.


NMR Structure Predictor


Text Editors


Emacs from the GNU pages

Emacs wiki

Gnu Emacs Manual

A nice Emacs guide for beginners


Vim - the most popular Vi clone, typically found in all Linux systems.

Nano: Easy to use alternative to Emacs and VI


Textpad - good shareware editor for Windows.

Notepad++ - greatsource code editor for Windows

TextWrangler - greatsource code editor for Mac


An overview of programming with an emphasis on academic computing. Includes easy-start guides for FORTRAN, C/C++, bash shell, and Perl in a linux environment, as well as links to LATEX, php, HTML, awk resources and more

Fortran Tutorial

Gnu Debug debugger

Hints for Fortran programmers

Prof. Langsam Computer Science Courses, Brooklyn College


Codeblocks: Easy-to-use Internal Development Environment for C, C++, and Fortran 90

Intel Compilers for students

Operating systems

An overview with an emphasis on academic computing; includes lots of intros and FAQs as well as a reference card.

The beginners area of

A one page linux manual (pdf download)

Unix tipsheet

Other utilities

The SQS Queueing System

Latex the Wikibook.

Short introduction to LaTeX from CTAN.

A collection of LaTeX tutorials.

TeX for the Impatient contents pdf.

The recommended way to install TeX on the Mac is to go through

Unix Software Packages for Mac




Suggested Downloads

These have been found on macports, but are probably also in the other packages.
You may also need to download xquartz or x11.
These instructions for setting up Macports, then Python through Macports are recommended.

  • tree

creates a tree out of the ls command

  • openmpi

special compiler

  • xpdf

open pdf from the terminal

  • dos2unix

convert between old mac, pc, and linux file types.

  • gcc47

gfortran, gcc, g++, and similar compilers

  • grace

graphing software to use from terminal

  • xmgr

older version of grace if it the newerdoes not work
If it prints a lot of uninteresting complaints, use
xmgr 2> /dev/null
to suppress them.

  • gnuplot

alternative graphing software to use from terminal
If gnuplot from macports keeps upgrading from version 4 to 5 without you wanting it, you can undo it this way with the full name of whatever gnuplot version you are using instead of the one below:
sudo port activate gnuplot @4.6.5_2+aquaterm+luaterm+pangocairo+wxwidgets+x11

  • xclock

analog clock

  • openbabel

converts between chemical file types

  • pymol

software for viewing molecules, especially biomolecules

  • py27-openbabel

python chemistry related software

  • py27-scientific

python scientific related software

  • fdupes

checks for duplicate files in your directory system

  • py34-numpy
  • py34-matplotlib +tkinter

These commands will let you use the python3.4 command to to launch GaussSum 3, mentioned above in Electronic Structure.

  • ImageMagick

terminal commands for manipulating photos

  • rmtrash

alternative to rm that moves files to Mac's trash

  • poppler

gives you the pdfunite command to combine pdf documents, as described at this link.

  • xorg-server demeter

software for viewing EXAFS spectra. This may require the use of the following Macport, which should be reinstalled (courtesy, Mikhail Askerka):

  • xorg-libXt +flat_namespace
  • py27-pip
  • py34-pip

These commands will set up pip on your computer without needing to do it outside of Macports as suggested here. Afterwords, you should run the command:
sudo port select --set pip pip27 or sudo port select --set pip pip34 to get it to work. Then for some applications (courtesy, Mikhail Askerka) you may also need to add python modules as shown below:
pip install --upgrade ase
pip install --upgrade numpy scipy matplotlib

To get these python commands to work, adding these export statements to your .bash_profile would help:
export PYTHONPATH=/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages:$PYTHONPATH
export PATH=/opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin:$PATH

  • py27-pygtk

This Macport will run you run some aspects of ASE which allow for the visualization of solid structures.

Suggested Aliases and Other Additions to your Command Line (comments in bold)

Note: Put these in your ~/.bash_profile file and then use the source command on that to make it active.

alias gasum='python3.4 /Applications/GaussSum-3.0.1/'
This will run GaussSum for you if you installed python via Macports as described above.
You can also install the previous version of GaussSum and run it by
alias gasum2='python2.7 /Applications/GaussSum-'

alias avo='open -a /Applications/[NameOfApplication].app'
Note: replace "[NameOfApplication]" with the name of the .app file, such as Avogadro, to be able to use this command to open programs from the terminal

alias bc='bc -l'
Note: enables bc to start with full Math available e.g. 1/2 will be 0.5 not 0

alias [firstletterofcommand]old='history | grep command | tail
Note: replace "[firstletterofcommand]" to make a short shortcut command to find this first command in your history

alias gibbs='grep "Sum of electronic and thermal Free Energies" '
alias scf='grep "SCF Done" '
Note: replace "finds the free energy (top) or electronic energy (bottom) in a Gaussian output file that is the 1st argument after this command

alias graph='for f in *gpt ; do echo $f ; gnuplot < $f ; done ; open *eps'
Note: lets you graph all the Gnuplot files in your folder and open them.

alias ll='ls -lrth'
Note: Our preferred form of the ls command

alias sftp[Server]='sftp [username]@[Server]'
alias to[Server]='ssh [username]@[Server]'
Note: Let's you do the sftp (top) and ssh (bottom) command fast if you replace [username] and [Server]' appropriately

alias siestaE='find . -name \*.out -exec egrep -H '\''siesta: Total'\'' {} \;'
Note: Let's you find the final energy in all output files from SIESTA in the current folder and its child folders

alias tst='grep "Frequencies --" '
Note: Let's you find the frequencies in your Gaussian output file (1st argument)

alias vmd='/Applications/VMD/VMD\'
Note: Let's you open VMD from the terminal if you installed it with the above path

function tab_title {
echo -n -e "\033]0;${PWD##*/}\007"

Note: Let's you open new tabs that have the name of the current folder (not full path) in the tab title

Note: Has the prompt that precedes your typing in the terminal give the full path to your current folder

export PATH=/opt/local/bin:/opt/local/sbin:$PATH
Note: Required for MacPorts to work properly

Computational Chemistry Courses and Tutorials

Prof. Batista's Lecture Notes and Solutions to Problems, 2006 Summer School on Computational Materials Science (MCC-UIUC), Yale University.

Prof. Batista's classes and tutorials, Yale University.

Prof. Preskill's CS/Phys 229, Caltech.

Course on Computational Chemistry

Computational Chemistry Course, Minnesota. Contains problem sets and exams, useful for independent newbies.

Computational Chemistry, Joel Bowman

Computational Quantum Mechanics of Molecular and Extended Systems, MIT Fall 2004

Computational chemistry course at Cornell

Oviedo Quantum Chemistry Group software

Burkard Schmidt

Dave Young's topics, including a first-timer's guide to Gaussian and other useful monologues

Wave Package Demo

Macromolecular Simulation

PY 502, Computational Physics (Fall 2005) Anders Sandvik, Department of Physics, Boston University.

The CCCBDB, contains links to Experimental and computational thermochemical data for a selected set of 684 gas-phase atoms and molecules, and has some nice resources like a glossary and a description of the thermochemical quantities and methods.

Gaussian keywords

Gaussian pedagogical links

Computational Chemistry Wiki Contains computational results for selected molecules.

Tutorial for using Gaussian with Avogadro.

Recommended Books

C++ Language

Langsam, Yedidyah. Workbook for C++. 3rd Edition. Pearson Learning Solutions, 2009. ISBN: 0558347533, 9780558347536.

Jones, Jacqueline A., Keith Harrow. Problem Solving with C++. 2nd Edition. Pearson Custom Publishing, 2009. ISBN: 0558206514, 978-0558206512.

Liberty, Jesse. Sam's Teach Yourself C++ in 21 Days. 3rd Edition. Sams Publishing, 1999. ISBN: 0672315645, 9780672315640.

Fortran Language

Nyhoff, Larry, Sanford Leestma. FORTRAN 90 for Engineers and Scientists. 1st Edition. Pearson, 1996. ISBN: 0135197295, 9780135197295.

LaTeX Language

Kopka, Helmut, Patrick W. Daly. Guide to LaTeX. 4th Edition. Addison-Wesley Professional, 2003. 0321173856, 9780321173850.

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