output_bonds

Prints out all interactions in the system.

Usage:

python output_bonds.py input_file trajectory_file [confid]

Args:

• input_file: path to input file used for simulation
• trajectory_file: path to trajectory file generated from simulation
• confid: configuration id in the trajectory (defaults to 0, i.e. the first configuration)

Notes:

This script is only suitable for analysing a few configurations in a trajectory.

If you want to analyse the whole trajectory, you should use the DNAnalysis program directly. It can be found in the same place as the oxDNA executable.