UsefulLinks
Chemistry
Specialized Chemistry
Computational Chemistry
1. Introduction to Computational Chemistry
2. Mathematical and Physical Foundations
3. Potential Energy Surfaces
4. Molecular Mechanics Methods
5. Quantum Mechanical Methods
6. Molecular Dynamics Simulations
7. Monte Carlo Methods
8. Energy Minimization and Optimization
9. Hybrid and Multiscale Methods
10. Property Calculations
11. Solvation and Environmental Effects
12. Free Energy Methods
13. Excited States and Photochemistry
14. Solid State and Materials
15. Computational Tools and Software
16. High-Performance Computing
17. Best Practices and Validation
6.
Molecular Dynamics Simulations
6.1.
Theoretical Foundation
6.1.1.
Classical Equations of Motion
6.1.2.
Phase Space Trajectories
6.1.3.
Ergodic Hypothesis
6.1.4.
Time Averages vs Ensemble Averages
6.2.
Numerical Integration
6.2.1.
Finite Difference Methods
6.2.2.
Verlet Algorithm
6.2.3.
Leap-Frog Algorithm
6.2.4.
Velocity Verlet Algorithm
6.2.5.
Time Step Selection
6.2.6.
Stability and Accuracy
6.3.
Simulation Setup
6.3.1.
Initial Configurations
6.3.2.
Velocity Assignment
6.3.3.
Maxwell-Boltzmann Distribution
6.3.4.
Equilibration Procedures
6.4.
Boundary Conditions
6.4.1.
Periodic Boundary Conditions
6.4.2.
Minimum Image Convention
6.4.3.
Box Shapes and Geometries
6.4.4.
Surface Effects
6.5.
Statistical Ensembles
6.5.1.
Microcanonical Ensemble
6.5.2.
Canonical Ensemble
6.5.3.
Isothermal-Isobaric Ensemble
6.5.4.
Grand Canonical Ensemble
6.6.
Temperature Control
6.6.1.
Velocity Scaling
6.6.2.
Berendsen Thermostat
6.6.3.
Nosé-Hoover Thermostat
6.6.4.
Andersen Thermostat
6.6.5.
Langevin Dynamics
6.7.
Pressure Control
6.7.1.
Berendsen Barostat
6.7.2.
Parrinello-Rahman Barostat
6.7.3.
Martyna-Tobias-Klein Barostat
6.7.4.
Isotropic and Anisotropic Scaling
6.8.
Trajectory Analysis
6.8.1.
Structural Properties
6.8.2.
Dynamic Properties
6.8.3.
Time Correlation Functions
6.8.4.
Radial Distribution Functions
6.8.5.
Mean Square Displacements
6.8.6.
Diffusion Coefficients
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5. Quantum Mechanical Methods
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7. Monte Carlo Methods