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#### Output

The results of an OP analysis are stored in a NetCDF file whose main variables are namely:

- time: the times in ps at which all the time-dependent OP is computed,
- bond: the index of the bonds selected for the analysis. In case where the system under study is the a protein or a peptide chain, this index is simply the sequence number of the first atom forming the bond, otherwise it is just an integer ranging from 1 to where is the number of selected bonds,
- p2: the order parameter P2 defined in Eq. 4.195,
- p2-bondavg: the bond-averaged P2 defined in Eq. 4.198,
- s2: the generalized order parameter defined above in section 4.2.7.1.