simulations

maybe someday… but not today.

• Theory / Methods Overview
  • Molecular Descriptors
  • Properties of Interest
  • Other Methods
  • Literature
    • 1. Binding Affinity
      • 1.1. Simulating Binding Affinity
    • 2. Classical Molecular Dynamics
      • 2.1. Potential Energy
      • 2.2. Force Fields
    • 3. FE Alchem
    • 4. Alchemical Free Energy
    • 5. Free Energy Estimators
    • 6. QM/MM Simulations
      • 6.1. Overview
      • 6.2. Bonded Interactions
      • 6.3. Nonbonded Interactions
      • 6.4. Electrostatic Embedding
        • 6.4.1. Short-Range
• Compile Notes
• Tutorial
• Analysis
  • 1. Pairwise RMSD
  • 2. Antechamber
  • 3. Export Dry Trajectory (no water)
  • 4. PCA with CPPTRAJ
  • 5. parmchk2.sh
  • 6. parmed
  • 7. Principal Component Analysis
  • 8. Plot PMF with PyMBAR
  • 9. RDF
  • 10. Root Mean Square Deviation (RMSD)
  • 11. Root Mean Square Fluctuation (RMSF)
  • 12. tleap