CHEM3300G

Computer Methods in Chemistry - CHEM3300G

Lectures

Week 1: Basic concepts
Week 2: Linux, Python and visualization
Week 3: First look into molecular dynamics
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

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Topic 7¶

Notes about topic 7.

Topic 6 Topic 8

By Mikko Karttunen
© Copyright Mikko Karttunen.

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