To initialize a trajectory file for computation, use the command

trajectory = Trajectory("trajectory.xtc",solute,solvent)

where solute and 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.

The 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.

Tip

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")
Note

The trajectory stream is closed at the end of the MDDF computation. Therefore if you want to reuse the same trajectory for another MDDF computation in the same script, you need to reload it. For example:

solute = Selection("system.pdb","protein",nmols=1)
# Compute the protein-water MDDF
solvent = Selection("system.pdb","water",natomspermol=3)
trajectory = Trajectory("trajectory.xtc",solute,solvent)
R_water = mddf(trajectory)
# Compute the protein-urea MDDF
solvent = Selection("system.pdb","resname URE",natomspermol=8)
trajectory = Trajectory("trajectory.xtc",solute,solvent)
R_urea = mddf(trajectory)