Forcefield-Based Simulations

List of Figures

Figure 1. Energy and probability of a mechanical and quantum particle in a harmonic energy well

Figure 2. Morse vs. harmonic potentials

Figure 3. Oxalic acid structure and CFF91 atom types

Figure 4. Torsion exocyclic to an aromatic ring

Figure 5. Distance and angle criteria for hydrogen bonds

Figure 6. Distance restraint function

Figure 7. Relationship between Cartesian coordinate system (xyz) and periodic system (abc) in Discover and CHARMm

Figure 8. Relationship between Cartesian coordinate system (xyz) and periodic system (abc) in Cerius2·OFF

Figure 9. Solute surrounded by solvent

Figure 10. Minimum-image model

Figure 11. Explicit-image model

Figure 12, Types of interactions usually excluded from nonbond calculations

Figure 13. Number of nonbond interactions as a function of cutoff distance

Figure 14. Van der Waals energy as a function of cutoff distance

Figure 15. Application of a switching function

Figure 16. Three-level hierarchical cell system

Figure 17. Electrostatic energy vs. cutoff distance for quartz

Figure 18. van der Waals energy vs. cutoff distance for NaCl

Figure 19. Energy contour surface of a simple function

Figure 20. Energy surface for Eq. 60

Figure 21. Cross section of the energy surface as defined by the intersection of the line search path in Figure 20 with the energy surface

Figure 22. Minimization path following a steepest-descents path

Figure 23. Minimization path following a steepest-descents path without line searches

Figure 24. General algorithm for variants of Newton-Raphson method

Figure 25. Flowchart of truncated Newton-Raphson method

Figure 26. Numerical integration of energy from molecular dynamics hydrogen-collision trajectory, 1 fs timestep

Figure 27. Numerical integration of energy from molecular dynamics hydrogen-collision trajectory, 0.33 and 0.1 fs timesteps

Figure 28. Numerical integration of energy from molecular dynamics hydrogen-collision trajectory, 2 fs timestep

Figure 29. Numerical integration of energy from molecular dynamics hydrogen-collision trajectory, 4 fs timestep

Figure 30. Integration errors for hydrogen-collision trajectories at several temperatures

Figure 31. Maxwell-Boltzmann distribution of velocity of water at various temperatures Figure 32. The ensemble-averaged quantity from Eq. 120 plotted vs. time for three values of

Figure 32. The ensemble-averaged quantity from Eq. 120 plotted vs. time for three values of Figure 33. Definitions of ₁ and

Figure 33. Definitions of 1 and 2 for fentanyl

Figure 34. Two-Dimensional energy map of fentanyl as a function of the two dihedral angles defined in Figure 33 Figure 35. Time history of the dihedral angles ₁ and

Figure 35. Time history of the dihedral angles 1 and 2 superimposed on the 2D energy map of Figure 34