simulations

maybe someday…. but not today.

• 1. Theory / Methods Overview
  • 1.1. Molecular Descriptors
  • 1.2. Properties of Interest
  • 1.3. Other Methods
  • 1.4. Literature
    • 1.4.1. Binding Affinity
      • 1.4.1.1. Simulating Binding Affinity
    • 1.4.2. Classical Molecular Dynamics
      • 1.4.2.1. Potential Energy
      • 1.4.2.2. Force Fields
    • 1.4.3. FE Alchem
    • 1.4.4. Alchemical Free Energy
      • 1.4.4.1. ::::{sidebar} :::{figure} ../../_static/images/fe-alchem-thermo-cycle.png
      • 1.4.4.2. align: center figwidth: 100%
    • 1.4.5. Free Energy Estimators
    • 1.4.6. QM/MM Simulations
      • 1.4.6.1. Overview
      • 1.4.6.2. Bonded Interactions
      • 1.4.6.3. Nonbonded Interactions
      • 1.4.6.4. Electrostatic Embedding
        • 1.4.6.4.1. Short-Range
• Compile Notes
• 2. Tutorial
• 3. Analysis
  • 3.1. Pairwise RMSD
  • 3.2. Antechamber
  • 3.3. Export Dry Trajectory (no water)
  • 3.4. PCA with CPPTRAJ
  • 3.5. parmchk2.sh
  • 3.6. parmed
  • 3.7. Principal Component Analysis
  • 3.8. Plot PMF with PyMBAR
  • 3.9. RDF
  • 3.10. Root Mean Square Deviation (RMSD)
  • 3.11. Root Mean Square Fluctuation (RMSF)
  • 3.12. tleap