Molecular dynamics: survey of methods for simulating the activity of proteins.

3.2. Energy Minimization 1592 3.3. Adiabatic Mapping 1593 3.4. Molecular Dynamics 1593 3.4.1. Simulated Environment 1595 3.4.2. SHAKE 1595 3.4.3. Experimental Conditions 1596 3.4.4. Solvation 1596 3.5. Langevin Dynamics 1597 3.6. Brownian Dynamics 1597 3.7. Monte Carlo 1598 3.8. Simulated Annealing 1598 3.9. Nondynamic Methods 1598 3.9.1. Conformational Sampling 1598 3.9.2. Principal Component Analysis 1598 3.10. QM/MM 1599 4. Free-Energy Calculations 1599 4.1. Free Energy of Binding 1599 4.2. Activated Molecular Dynamics 1600 4.3. Steered Molecular Dynamics 1600 5. Recent Advances in the Theoretical Aspects of Molecular Dynamics 1600