CHEM3300G
Computer Methods in Chemistry - CHEM3300G
Lectures
Week 1: Basic concepts
1. General aspects of modeling and computer simulations
2. Introduction to computational modeling & methods in chemistry/physics
3. Background on computers, computing and High Performance Computing
Week 2: Linux, Python and visualization
1. Linux - the basics
2. Basic Linux commands
3. More Linux commands
4. Brief introduction to Python
Week 3: First look into molecular dynamics
1. Molecular visualization and VMD
2. First look into particle simulations
3. Gromacs installation
Week 4: Simulation practicals
1. What is Molecular Dynamics (MD)
2. Introduction to Gromacs
Week 5: Analysis: Equilibrium and structure
1. Physical properties: Structure
Week 6: Interactions and force fields
Week 7: More analysis methods
Week 8: Multiscale modeling
Week 9: Modeling cells
Week 10: Quantum level
Week 11: Machine learning
Week 12: Machine learning
Week 13: Summary
LABS
Lab 1: Installation of tools.
Lab 2, part 1/2: Installation of Gromacs
Lab 2, part 2/2: Visualization of molecules using VMD
Lab 3: Simulation of water
Lab 4: Simulation of water 2: Physical properties of water
Lab 5: Simulation of lysozyme, part 1/2
More material
On computation and codes
Installation instructions
Installation of Python and Jupyter
Python virtual environments
VMD installation
VMD extras
VMD plugins
How-tos
Jupyter Notebook / Jupyter Lab
The
vi
editor
Editing ASCII files
Helpful software
Gallery
Gallery of pictures generated while preparing the course material
Index
