2. simulations

maybe someday… but not today.

• 2.1. Theory / Methods Overview
  • 2.1.1. Molecular Descriptors
  • 2.1.2. Properties of Interest
  • 2.1.3. Other Methods
  • 2.1.4. Literature
    • 2.1.4.1. Binding Affinity
      • 2.1.4.1.1. Simulating Binding Affinity
    • 2.1.4.2. Classical Molecular Dynamics
      • 2.1.4.2.1. Potential Energy
      • 2.1.4.2.2. Force Fields
    • 2.1.4.3. FE Alchem
    • 2.1.4.4. Alchemical Free Energy
    • 2.1.4.5. Free Energy Estimators
    • 2.1.4.6. QM/MM Simulations
      • 2.1.4.6.1. Overview
      • 2.1.4.6.2. Bonded Interactions
      • 2.1.4.6.3. Nonbonded Interactions
      • 2.1.4.6.4. Electrostatic Embedding
        • 2.1.4.6.4.1. Short-Range
• 2.2. Compile Notes
• 2.3. Tutorial
• 2.4. Analysis
  • 2.4.1. Pairwise RMSD
  • 2.4.2. Antechamber
  • 2.4.3. Export Dry Trajectory (no water)
  • 2.4.4. parmchk2.sh
  • 2.4.5. parmed
  • 2.4.6. Principal Component Analysis
  • 2.4.7. Plot PMF with PyMBAR
  • 2.4.8. RDF
  • 2.4.9. Root Mean Square Deviation (RMSD)