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Week 8Section 1

MD Fundamentals

Understanding molecular dynamics simulations

30-45 minSection0/1 Activities Complete
Overview

Understanding molecular dynamics simulations

Activities & Tasks
1

OpenMM Simulation

Set up and run molecular dynamics simulations

coding
Start
Week Resources

Required Readings

OpenMM Documentation
Read
MD Simulations overview
Read

Exercises

Coding Exercise

Run toy MD of alanine dipeptide with OpenMM

Visualization

Animate folding with NGLView (Jupyter)

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