TRJ, MDCRD, CRDBOX (AMBER ASCII trajectory)

Coordinate reader

MDAnalysis.coordinates.TRJ.TRJReader

MDAnalysis supports reading of AMBER ASCII trajectories (“traj”) and binary trajectories (“netcdf”).

Important

In the AMBER community, these trajectories are often saved with the suffix ‘.crd’. This extension conflicts with the CHARMM CRD format and MDAnalysis will not correctly autodetect AMBER “.crd” trajectories. Instead, explicitly provide the format="TRJ" argument to Universe:

u = MDAnalysis.Universe("top.prmtop", "traj.crd", format="TRJ")

Reading in

Units are assumed to be the following default AMBER units:

• length: Angstrom

• time: ps