Intro to Molecular Simulations

Overview

Welcome to the Intro to Molecular Simulations workshop!

This workshop will introduce molecular simulations, a powerful type of modeling with applications in many fields, including chemistry, biology, physics, medicine, and more. The theory behind two common forms of molecular modeling, molecular dynamics (MD) and Monte Carlo (MC), will be reviewed, and we will use Python to set up, run, and analyze these two types of simulations.

Duration: ~4 hours

Requirements

• Basic Python knowledge (syntax, file I/O)
• Access to Google Colab

Sofware

• Please ensure that you have a Google account to use Google Colab.

Outline

• Introduction to Molecular Simulation
  • The Ergodic Theorem
  • Statistical Mechanics - Averaging
• Monte Carlo (MC) Simulations
  • Basics of MC (Boltzmann distribution, MC algorithm)
  • Hands-on: Performing an MC simulation in Python
• Molecular Dynamics (MD) Simulation
  • Basics of MD (force fields, MD algorithm)
  • Hands-on: Performing an MD simulation in Python
• Analyzing Molecular Simulations in Python
  • Hands-on: using ML to analyze MD trajectories

References

Material created by Meghana Munipalle

Workshop created as part of the QLS-McGill Initiative in Computational Medicine