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Management of Trajectories

The history of molecular dynamics calculations can be stored in the form of coordinate or velocity trajectory files. This chapter deals with reading, writing, manipulating, and analyzing molecular dynamics trajectories.

Trajectory Definitions
Reading Trajectories
- Syntax
- Example
Writing Trajectories
Merging Trajectories
Analysis of Trajectories
Average Coordinates and Fluctuations
- Syntax
- Example
Density Analysis
- Syntax
Covariance Analysis
- Syntax
- Example
Time Correlation Analysis
- Syntax
Radial Distribution Functions
- Syntax
Angular Distribution Functions
- Syntax
Power Spectrum Analysis
- Syntax
Picking Properties for Trajectories
- Syntax

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