Busath Lab Molecular Dynamics

Welcome to the home page of Dr. David Busath’s Molecular Modeling and Dynamics course.

Packages / tools covered:

• CHARMM
• VMD
• NAMD
• WHAM

CHARMM Labs:

1. Introduction to the Protein Data Bank and VMD
2. Introduction to CHARMM
3. Molecular Structure and Manipulation
4. Energy Minimization
5. Introduction to Dynamics
6. Umbrella Sampling
7. Homology Modeling
8. Free-Energy Perturbation

NAMD (+ CHARMM) Labs:

1. Introduction to NAMD and Collective Variables
2. Building and Simulating a Protein-Bilayer System
3. Ligand Umbrella Sampling in a Protein-Bilayer System

Resources:

• Linux Cheatsheet
• Glossary

Contributors:

• Dr. David Busath: Labs 1-4, 6
• Richard Swensen: Various
• Mitchell Gleed: Lab 8, NAMD labs 1-3, Github pages
• Curtis Evans: Labs 7, 8
• Mark Fowler: Lab 7
• Matt Durrant: Lab 5