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3.1. Theory / Methods Overview
3.1.4.1. Binding Affinity
3.1.4.2. Classical Molecular Dynamics
3.1.4.3. FE Alchem
3.1.4.5. Free Energy Estimators
3.1.4.6. QM/MM Simulations
3.2. Compile Notes
3.2.1. Compile
helpmelib
executable
3.2.2. Patch / Compile
3.2.3. Install QMHub
3.2.4. TorchMDnet-ext Environment (CPU)
3.3. Tutorial
3.3.1. Simple MD Tutorial of Alanine Dipeptide
3.3.2. Applying Distance Restraints in Classical MD Simulations
3.3.3. QM/MM Simulation of the Claisen Rearrangment Reaction
3.4. Analysis
3.4.1. Export Dry Trajectory (no water)
3.4.2. Plot PMF with PyMBAR
3.4.3. Pairwise Distance Matrix
3.4.4. Principal Component Analysis
3.4.5. RDF
3.4.6. Root Mean Square Deviation (RMSD)
3.4.7. Root Mean Square Fluctuation (RMSF)
3.
simulations
3.3.
Tutorial
3.3.
Tutorial
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