Computational Chemistry

  1. Molecular Dynamics Simulations
    1. Theoretical Foundation
      1. Classical Equations of Motion
        1. Phase Space Trajectories
          1. Ergodic Hypothesis
            1. Time Averages vs Ensemble Averages
            2. Numerical Integration
              1. Finite Difference Methods
                1. Verlet Algorithm
                  1. Leap-Frog Algorithm
                    1. Velocity Verlet Algorithm
                      1. Time Step Selection
                        1. Stability and Accuracy
                        2. Simulation Setup
                          1. Initial Configurations
                            1. Velocity Assignment
                              1. Maxwell-Boltzmann Distribution
                                1. Equilibration Procedures
                                2. Boundary Conditions
                                  1. Periodic Boundary Conditions
                                    1. Minimum Image Convention
                                      1. Box Shapes and Geometries
                                        1. Surface Effects
                                        2. Statistical Ensembles
                                          1. Microcanonical Ensemble
                                            1. Canonical Ensemble
                                              1. Isothermal-Isobaric Ensemble
                                                1. Grand Canonical Ensemble
                                                2. Temperature Control
                                                  1. Velocity Scaling
                                                    1. Berendsen Thermostat
                                                      1. Nosé-Hoover Thermostat
                                                        1. Andersen Thermostat
                                                          1. Langevin Dynamics
                                                          2. Pressure Control
                                                            1. Berendsen Barostat
                                                              1. Parrinello-Rahman Barostat
                                                                1. Martyna-Tobias-Klein Barostat
                                                                  1. Isotropic and Anisotropic Scaling
                                                                  2. Trajectory Analysis
                                                                    1. Structural Properties
                                                                      1. Dynamic Properties
                                                                        1. Time Correlation Functions
                                                                          1. Radial Distribution Functions
                                                                            1. Mean Square Displacements
                                                                              1. Diffusion Coefficients

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                                                                            5. Quantum Mechanical Methods

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                                                                            7. Monte Carlo Methods