About this Site
My colleagues asked for my research guides to be put on the Internet. This is my first attempt at doing that.
About the Guides
The guides were adapted from the manuals that Dr. Bill Miller III provides his undergraduate research students. They’ve evolved a bit since then.
The Unix Guide gives an overview of UNIX systems and basic commands to get someone started with using the command line. A PDF of this guide is available here.
The AMBER Guide covers how to set-up AMBER simulations and a general overview of molecular dynamics simulations. A PDF of this guide is available here.
The Simulation Analysis Guide addresses how to use some of the tools to analyze AMBER trajectories, visualizing data, and presenting data in a useful manner through images and videos. A PDF of this guide is available here.
The R Guide includes some basics for getting started with the R programming language. A PDF of this guide is available here.
Resources, Resources, Resources
There are a lot of resources for getting started with computational chemistry, and I’ve outlined a few here.
Tutorials
- UNIX/Linux Tutorial for Beginners
- AMBER Tutorials
- Data Carpentry (online lessons under development – ft. genomics!)
- Software Carpentry (online lessons)
- MolSSI: Getting Started in Computational Chemistry
- Overleaf: Learn LaTeX
Software/Programs
Terminal Emulators
Mac and Linux both come with a Terminal application, however, some users may prefer to use a different emulator instead. Windows users must use an emulator, as there is no native Terminal.
Free (at least for academic use)
Documentation
- AMBER
- CAVER
- Gaussian
- Gnuplot
- LICHEM
- MDAnalysis (Python package)
- MDTraj (Python package)
- OpenMM
- Psi4
- Tinker
- UCSF Chimera
- UNIX vi Editor Commands
- Visual Molecular Dynamics (VMD)
Cheat Sheets
Search Directories
Explanations and Lessons
- Mobley Lab: Basic (MD/MC) Simulation Training
- Shodor: Background Reading for Basis Sets
- Spartan’s Description of Basis Sets
- Dr. Sherrill: Basis Sets in Quantum Chemistry
- Dr. Gilbert: Introduction to Computational Quantum Chemistry
- Dr. Kahn: Semiempirical Quantum Chemistry
- Dr. Lynch: Introduction to GaussView and Gaussian