To initialize a trajectory file for computation, use the command
trajectory = Trajectory("trajectory.xtc",solute,solvent)
solvent are defined with the
Selection function described before. This function opens the stream for reading frames, which are read once a time when the coordinates are required for computing the MDDF.
Trajectory function uses Chemfiles in background, and thus the most common trajectory formats are supported, as the ones produced with NAMD, Gromacs, LAMMPS, Amber, etc.
The format of the trajectory file is automatically determined by Chemfiles from the extension of the file. However, it can be provided by the user with the
format keyword, for example:
trajectory = Trajectory("trajectory.xtc",solute,solvent,format="xtc")