Next: Mean-Square Displacement Up: The Analysis menu Previous: Running modes Contents

##
The Dynamics menu

Pressing the button Dynamics brings up a menu from which it is possible to choose the following analysis:

- Mean-Square Displacement
- Root Mean-Square Displacement
- Radius Of Gyration
- Velocity AutoCorrelation Function
- Density Of States
- Pass-Band Filtered Trajectory
- Global Motion Trajectory
- Center Of Mass Trajectory
- Rigid-Body Trajectory
- Center Of Mass Trajectory
- Auto-Regressive Analysis
- Quasi-Harmonic Analysis
- Reorientational Correlation Function
- Angular Velocity AutoCorrelation Function
- Angular Density Of States

Subsections

- Mean-Square Displacement
  - Theory and implementation
  - Parameters
  - Output
- Root Mean-Square Deviation
  - Theory and implementation
  - Parameters
  - Output
- Radius of gyration
  - Theory and implementation
  - Parameters
  - Output
- Angular Correlation
  - Theory and implementation
  - Parameters
  - Output
- Velocity Autocorrelation Function
  - Theory and implementation
  - Parameters
  - Output
- Density Of States
  - Theory and implementation
  - Parameters
  - Output
- Pass-Band Filtered Trajectory
  - Theory and implementation
  - Parameters
  - Output
- Global Motion Filtered Trajectory
  - Theory and implementation
  - Parameters
  - Output
- Rigid-Body Trajectory
  - Theory and implementation
    - Optimal superposition.
    - Quaternions and rotations.
    - Solution of the minimization problem.
  - Parameters
  - Output
- Center Of Mass Trajectory
  - Theory and implementation
  - Parameters
  - Output
- Auto-Regressive Analysis
  - Theory and implementation
    - VACF within the AR model
    - Density of states within the AR model
    - Discrete memory function of the VACF within the AR model
    - MSD within the AR model
    - Friction coefficient within the AR model
  - Parameters
  - Output
- Quasi Harmonic Analysis
  - Theory and implementation
  - Parameters
  - Output
- Reorientational Correlation Function
  - Theory and implementation
  - Parameters
  - Output
- Angular Velocity AutoCorrelation Function
  - Theory and implementation
  - Parameters
  - Output
- Angular Density Of States
  - Theory and implementation
  - Parameters
  - Output