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  • Week 1
  • Week 2
  • Week 3
    • Lecture: Dynamical Properties
    • Lecture: Thermostats
    • Lab: Data Analysis
    • Lab: Running vacuum MD
    • Assignment 5
  • Week 4
  • Week 5
  • Files
  • Chem 181 Troubleshooting Guide and Tips

CHEM 181

Introduction to Molecular Simulation

During week three we will accomplish these main objectives:

  • Learn how to perform advanced data analysis.
  • Learn how the molecular dynamics simulation software NAMD works.
  • Learn how to prepare and run a simple NAMD simulation in the absence of any solvent (a vacuum simulation).
  • New! Prepare for Week 4!

  1. Assignment 5
  2. FileSet3.tar.gz
  3. FileSet3.zip

In addition, more background reading needs to be completed:
  • Cramer Part 4
  • Cramer Part 5
  • CHARMM Force Field

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