Distance Measurement for One Trajectory

  1. Go to the directory containing the “trajectory_anneal.xyz” file.
  2. If measure distances between atom C18 and N12, O24 and H26, N13 and H28, run command ~/mopac/traj2measure cur C18-N12 O24-H26 N13-H28. Each atomic pair is separated with a whitespace and two atoms are separated with a hyphen (“-“).
  3. Edit the time, partition and account in “submit_measure.sh” if needed.
  4. Submit the submission file: sbatch submit_measure.sh
  5. You should be able to see your output file measure.log in one minute!

Distance Measurement for Multiple Trajectories

  1. If multiple direct sub-directories containing “trajectory_anneal.xyz” files, go to the parent directory of these sub-directories.
  2. To measure distances between atom C18 and N12, O24 and H26, N13 and H28, run command ~/mopac/traj2measure sub C18-N12 O24-H26 N13-H28.
  3. Remaining steps are same with the above section.