McCarty Group Wiki
This wiki is intended as a place to host introductory material and tutorials about running molecular dynamics simulations, methods and protocols of the group, and other useful materials for performing computational research. If you are new to the group, please be sure to read the UNIX commands for computational chemistry and the Basics of a GROMACS simulation.
A number of tutorials are provided to help new undergraduate research students in the group get training on particular methods and to get an idea of the nature of computational research in our lab.
Molecular Dynamics
Introduction to MD simulation: Liquid Argon
Basics of a GROMACS simulation
Analyzing an MD simulation
Protein-Ligand complex
Enhanced Sampling Approaches
Metadynamics
Replica Exchange MD
Umbrella Sampling
Molecular Docking
Quantum Chemistry
Geometry Optimization
RESP Charge Fitting
ab initio MD and QM/MM
AIMD water using CP2K
QM/MM of enzyme using CP2K
Other useful pages
UNIX commands for computational chemistry
Using Github
Making High Quality Figures in VMD
Converting between Amber and GROMACS format
Test Page