3. simulations# maybe someday…. but not today. 3.1. Theory / Methods Overview 3.1.1. Molecular Descriptors 3.1.2. Properties of Interest 3.1.3. Other Methods 3.1.4. Literature 3.1.4.1. Binding Affinity 3.1.4.1.1. Simulating Binding Affinity 3.1.4.2. Classical Molecular Dynamics 3.1.4.2.1. Potential Energy 3.1.4.2.2. Force Fields 3.1.4.3. FE Alchem 3.1.4.4. Alchemical Free Energy 3.1.4.4.1. ::::{sidebar} :::{figure} ../../_static/images/fe-alchem-thermo-cycle.png 3.1.4.4.2. align: center figwidth: 100% 3.1.4.5. Free Energy Estimators 3.1.4.6. QM/MM Simulations 3.1.4.6.1. Overview 3.1.4.6.2. Bonded Interactions 3.1.4.6.3. Nonbonded Interactions 3.1.4.6.4. Electrostatic Embedding 3.1.4.6.4.1. Short-Range 3.2. Compile Notes 3.3. Tutorial 3.4. Analysis 3.4.1. Pairwise RMSD 3.4.2. Antechamber 3.4.3. Export Dry Trajectory (no water) 3.4.4. parmchk2.sh 3.4.5. parmed 3.4.6. Principal Component Analysis 3.4.7. Plot PMF with PyMBAR 3.4.8. RDF 3.4.9. Root Mean Square Deviation (RMSD)
