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# 5.11. AMBER trajectories — `MDAnalysis.coordinates.TRJ`

AMBER can write ASCII trajectories (“traj”) and binary trajectories (“netcdf”). MDAnalysis supports reading of both formats and writing for the binary trajectories.

Note

Support for AMBER is experimental and feedback and contributions are highly appreciated. Use the Issue Tracker or get in touch on the MDAnalysis mailinglist.

Units

- lengths in Angstrom (Å)
- time in ps (but see below)

AMBER trajectory coordinate frames are based on a `Timestep` object.

class `MDAnalysis.coordinates.TRJ.``Timestep`(arg, **kwargs)

  AMBER trajectory Timestep.

  The Timestep can be initialized with arg being

  1. an integer (the number of atoms) and an optional keyword argument velocities to allocate space for both coordinates and velocities;
  2. another `Timestep` instance, in which case a copy is made (If the copied Timestep does not contain velocities but velocities = `True` is provided, then space for velocities is allocated);
  3. a `numpy.ndarray` of shape `(numatoms, 3)` (for positions only) or `(numatoms, 6)` (for positions and velocities): `positions = arg[:,:3]`, `velocities = arg[:3:6]`.
  `_pos`

    coordinates of the atoms as a `numpy.ndarray` of shape (numatoms, 3)

  `_velocities`

    velocities of the atoms as a `numpy.ndarray` of shape (numatoms, 3); only available if the trajectory contains velocities or if the velocities = `True` keyword has been supplied.

  `dimensions`

    unitcell dimensions (A, B, C, alpha, beta, gamma)

    - A, B, C are the lengths of the primitive cell vectors e1, e2, e3
    - alpha = angle(e1, e2)
    - beta = angle(e1, e3)
    - gamma = angle(e2, e3)

    Note

    A ASCII AMBER trajectory only contains box lengths A,B,C; we assume an orthorhombic box and set all angles to 90º.

## 5.11.1. ASCII TRAJ trajectories

ASCII AMBER TRJ coordinate files (as defined in AMBER TRJ format) are handled by the `TRJReader`. It is also possible to directly read bzip2 or gzip compressed files.

AMBER ASCII trajectories are recognised by the suffix ‘.trj’ or ‘.mdcrd’ (possibly with an additional ‘.gz’ or ‘.bz2’).

Limitations

- 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 as kwarg delta)
- No direct access of frames is implemented, only iteration through the trajectory.
- 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).

class `MDAnalysis.coordinates.TRJ.``TRJReader`(filename, numatoms=None, **kwargs)

  AMBER trajectory reader.

  Reads the ASCII formatted AMBER TRJ format. Periodic box information is auto-detected.

  The number of atoms in a timestep must be provided in the numatoms keyword because it is not stored in the trajectory header and cannot be reliably autodetected. The constructor raises a `ValueError` if numatoms is left at its default value of `None`.

  The length of a timestep is not stored in the trajectory itself but can be set by passing the delta keyword argument to the constructor; it is assumed to be in ps. The default value is 1 ps.

  Functionality is currently limited to simple iteration over the trajectory.

  `close`()

    Close trj trajectory file if it was open.

  `numframes`

    Number of frames (obtained from reading the whole trajectory).

  `open_trajectory`()

    Open the trajectory for reading and load first frame.

  `rewind`()

    Reposition at the beginning of the trajectory

## 5.11.2. Binary NetCDF trajectories

The AMBER netcdf format make use of NetCDF (Network Common Data Form) format. Such binary trajectories are recognized in MDAnalysis by the ‘.ncdf’ suffix and read by the `NCDFReader`.

Binary trajectories can also contain velocities and can record the exact time step. In principle, the trajectories can be in different units than the AMBER defaults of ångström and picoseconds but at the moment MDAnalysis only supports those and will raise a `NotImplementedError` if anything else is detected.

class `MDAnalysis.coordinates.TRJ.``NCDFReader`(filename, numatoms=None, **kwargs)

  Reader for AMBER NETCDF format (version 1.0).

  AMBER binary trajectories are automatically recognised by the file extension ”.ncdf”.

  The number of atoms (numatoms) does not have to be provided as it can be read from the trajectory. The trajectory reader can randomly access frames and therefore supports direct indexing (with 0-based frame indices) and full-feature trajectory iteration, including slicing.

  Velocities are autodetected and read into the `Timestep._velocities` attribute.

  Periodic unit cell information is detected and used to populate the `Timestep.dimensions` attribute. (If no unit cell is available in the trajectory, then `Timestep.dimensions` will return `[0,0,0,0,0,0]`.)

  Current limitations:

  - only trajectories with time in ps and lengths in Angstroem are processed
  - scale_factors are not supported (and not checked)

  See also

  `NCDFWriter`

  `__getitem__`(frame)

    Return the Timestep corresponding to frame.

    If frame is a integer then the corresponding frame is returned. Negative numbers are counted from the end.

    If frame is a `slice` then an iterator is returned that allows iteration over that part of the trajectory.

    Note

    frame is a 0-based frame index.

  `__iter__`()

    Iterate over the whole trajectory

  `Writer`(filename, **kwargs)

    Returns a NCDFWriter for filename with the same parameters as this NCDF.

    All values can be changed through keyword arguments.

    Arguments : | filename filename of the output NCDF trajectory
    Keywords : | numatoms number of atoms delta length of one timestep in picoseconds remarks string that is stored in the title field
    Returns : | `NCDFWriter`

  `close`()

    Close trajectory; any further access will raise an `IOError`

class `MDAnalysis.coordinates.TRJ.``NCDFWriter`(filename, numatoms, start=0, step=1, delta=1.0, remarks=None, convert_units=None, zlib=False, cmplevel=1)

  Writer for AMBER NETCDF format (version 1.0).

  AMBER binary trajectories are automatically recognised by the file extension ”.ncdf”.

  Velocities are written out if they are detected in the input `Timestep`. The trajectories are always written with ångström for the lengths and picoseconds for the time (and hence Å/ps for velocities).

  Unit cell information is written if available.

  See also

  `NCDFReader`

  Create a new NCDFWriter

  Arguments : | filename name of output file numatoms number of atoms in trajectory file
  Keywords : | start starting timestep step skip between subsequent timesteps delta timestep convert_units `True`: units are converted to the AMBER base format; `None` selects the value of `MDAnalysis.core.flags` [‘convert_gromacs_lengths’]. (see Flags) zlib compress data [`False`] cmplevel compression level (1-9) [1]

  `is_periodic`(ts=None)

    Return `True` if `Timestep` ts contains a valid simulation box

  `write_next_timestep`(ts=None)

    write a new timestep to the trj file

    ts is a `Timestep` instance containing coordinates to be written to trajectory file

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