Analyzing a part of the trajectory

By default, gorder analyzes the entire provided trajectory, meaning it processes all frames from the start to the end of the trajectory.

If you want to analyze only a specific part of the trajectory, you can use the begin, end, and step options to control the time range and frequency of analysis.

• begin: Specifies the time (in ps) from which the trajectory will start being read.
• end: Specifies the time (in ps) at which the trajectory analysis will stop.
• step: Specifies the step size for reading trajectory frames (i.e., how often a frame will be analyzed).

Example: Calculating coarse-grained order parameters from a specific part of a trajectory

structure: system.tpr
trajectory: md.xtc
analysis_type: !CGOrder
  beads: "@membrane"
begin: 100000.0
end: 300000.0
step: 5
output: order.yaml

In this example, the analysis starts at time 100,000 ps (100 ns) and ends at time 300,000 ps (300 ns). Every 5th frame of the trajectory will be analyzed.