Coordinate reader


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


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


  • Periodic boxes are only stored as box lengths A, B, C in an AMBER trajectory; the reader always assumes that these are orthorhombic boxes.

  • The trajectory does not contain time information so we simply set the time step to 1 ps (or the user could provide it with the dt argument)

  • Trajectories with fewer than 4 atoms probably fail to be read (BUG).

  • If the trajectory contains exactly one atom then it is always assumed to be non-periodic (for technical reasons).

  • Velocities are currently not supported as ASCII trajectories.