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  • quickstart
  • command line
  • HPC
  • python
  • simulation
  • More Notes !!
  • Google Scholar
  • GitHub
  • Twitter
  • Linkedin

Section Navigation

  • 1. Theory / Methods Overview
  • 6. Tutorial
    • 6.1. Simple MD Tutorial of Alanine Dipeptide
    • 6.2. Applying Distance Restraints in Classical MD Simulations
    • 6.3. QM/MM Simulation of the Claisen Rearrangment Reaction
  • 7. Analysis
    • 7.1. Pairwise RMSD
    • 7.2. Antechamber
    • 7.3. Export Dry Trajectory (no water)
    • 7.4. parmchk2.sh
    • 7.5. parmed
    • 7.6. Principal Component Analysis
    • 7.7. Plot PMF with PyMBAR
    • 7.8. RDF
    • 7.9. Root Mean Square Deviation (RMSD)
    • 7.10. Root Mean Square Fluctuation (RMSF)
    • 7.11. tleap
  • simulation

simulation#

  • 1. Theory / Methods Overview
  • 2. Molecular Descriptors
  • 3. Properties of Interest
  • 4. Other Methods
  • 5. Literature
  • 6. Tutorial
  • 7. Analysis

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