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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).

  • Assignment 5
  • FileSet3.tar.gz
  • FileSet3.zip

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

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